From efb0c4be5b5d421348d5840352aa0fc0b433d7e7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:12:19 +0000
Subject: [PATCH 01/54] Bump commons-cli:commons-cli from 1.6.0 to 1.7.0
 (#11236)

Bumps commons-cli:commons-cli from 1.6.0 to 1.7.0.

---
updated-dependencies:
- dependency-name: commons-cli:commons-cli
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a0d3ede962a..371cedbe395 100644
--- a/build.gradle
+++ b/build.gradle
@@ -170,7 +170,7 @@ dependencies {
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.78'
 
-    implementation 'commons-cli:commons-cli:1.6.0'
+    implementation 'commons-cli:commons-cli:1.7.0'
 
     implementation 'org.libreoffice:unoloader:7.6.4'
     implementation 'org.libreoffice:libreoffice:7.6.4'

From 310d002059c0adaf5594efd767c96070fcdf6a14 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:12:38 +0000
Subject: [PATCH 02/54] Bump de.undercouch:citeproc-java from 3.0.0 to 3.1.0
 (#11235)

Bumps [de.undercouch:citeproc-java](https://github.com/michel-kraemer/citeproc-java) from 3.0.0 to 3.1.0.
- [Release notes](https://github.com/michel-kraemer/citeproc-java/releases)
- [Commits](https://github.com/michel-kraemer/citeproc-java/compare/3.0.0...3.1.0)

---
updated-dependencies:
- dependency-name: de.undercouch:citeproc-java
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 371cedbe395..8913346967d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -240,7 +240,7 @@ dependencies {
     // route all requests to log4j to SLF4J
     implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.1'
 
-    implementation('de.undercouch:citeproc-java:3.0.0') {
+    implementation('de.undercouch:citeproc-java:3.1.0') {
         exclude group: 'org.antlr'
     }
 

From 0914336123147cbc009581aa712e8b4218845964 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:19:38 +0000
Subject: [PATCH 03/54] Bump org.slf4j:slf4j-api from 2.0.12 to 2.0.13 (#11238)

Bumps org.slf4j:slf4j-api from 2.0.12 to 2.0.13.

---
updated-dependencies:
- dependency-name: org.slf4j:slf4j-api
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8913346967d..1746b63f006 100644
--- a/build.gradle
+++ b/build.gradle
@@ -230,7 +230,7 @@ dependencies {
     implementation 'org.jsoup:jsoup:1.17.2'
     implementation 'com.konghq:unirest-java:3.14.5'
 
-    implementation 'org.slf4j:slf4j-api:2.0.12'
+    implementation 'org.slf4j:slf4j-api:2.0.13'
     implementation "org.tinylog:tinylog-api:2.7.0"
     implementation "org.tinylog:slf4j-tinylog:2.7.0"
     implementation "org.tinylog:tinylog-impl:2.7.0"

From 7fd88d5a089c11a529f77e3c010b85495c841705 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:20:53 +0000
Subject: [PATCH 04/54] Bump org.bouncycastle:bcprov-jdk18on from 1.78 to
 1.78.1 (#11237)

Bumps [org.bouncycastle:bcprov-jdk18on](https://github.com/bcgit/bc-java) from 1.78 to 1.78.1.
- [Changelog](https://github.com/bcgit/bc-java/blob/main/docs/releasenotes.html)
- [Commits](https://github.com/bcgit/bc-java/commits)

---
updated-dependencies:
- dependency-name: org.bouncycastle:bcprov-jdk18on
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 1746b63f006..76c0d2cefcb 100644
--- a/build.gradle
+++ b/build.gradle
@@ -168,7 +168,7 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.2.224'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.78'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.78.1'
 
     implementation 'commons-cli:commons-cli:1.7.0'
 

From 0f9e0e74268dd0adb56866c04694dddb8b6f3527 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:34:52 +0000
Subject: [PATCH 05/54] Bump src/main/resources/csl-styles from `d9ca259` to
 `af6f50b` (#11240)

Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `d9ca259` to `af6f50b`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](https://github.com/citation-style-language/styles/compare/d9ca25977a10d6717d0fc219c1b982863a23a0e7...af6f50b080190ccc7ba0c83906fe36c5ece85ce5)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-styles
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 src/main/resources/csl-styles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
index d9ca25977a1..af6f50b0801 160000
--- a/src/main/resources/csl-styles
+++ b/src/main/resources/csl-styles
@@ -1 +1 @@
-Subproject commit d9ca25977a10d6717d0fc219c1b982863a23a0e7
+Subproject commit af6f50b080190ccc7ba0c83906fe36c5ece85ce5

From dbd9257947147591706c6e0ab6d04aee161bd4e7 Mon Sep 17 00:00:00 2001
From: Jean Perbet <jeanperbet@icloud.com>
Date: Tue, 23 Apr 2024 11:33:27 +0200
Subject: [PATCH 06/54] Keep {} in Markdown rendering (#11196)

* fix: removed '{' and '}' swallow when not in command in HTMLChars and adapted tests

* doc: updated CHANGELOG.md

* fix: added old test cases and adapted them to apply requested changes

* fix: fixed small rule in HTMLChars formatter to fix faulty tests

* test: added test case in MardownFormatterTest for string with braces

* test: added more test cases in MarkdownFormatterTest

* fix: fixed checkstyle erros in HTMLChars

* test: added test about code between quotes in MardownFormatterTest

* feat: added parameter to keep braces to HTMLChars

* feat: modified default preview to keep braces when formatting markdown

* test: added parameterized test cases to MardownFormatterTest, updated preferences migrations and made keep braces mode name more clear in HTMLChars

* fix: fixed issue about preferences migrations

* fix: rolling back modif. in HTMLCharsTest and enabled case-insensitive equality for braces keep mode in HTMLChars

* test: added test for markdown lists in MarkdowFormatterTest
---
 CHANGELOG.md                                  |  1 +
 .../jabref/logic/layout/format/HTMLChars.java | 33 +++++--
 .../migrations/PreferencesMigrations.java     |  1 +
 .../jabref/preferences/JabRefPreferences.java |  2 +-
 .../logic/layout/format/HTMLCharsTest.java    | 24 ++++++
 .../layout/format/MarkdownFormatterTest.java  | 85 +++++++++++++++----
 .../migrations/PreferencesMigrationsTest.java |  4 +-
 7 files changed, 123 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3c2d37b3e28..99fc9dfa8fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Fixed
 
 - We fixed an issue where entry type with duplicate fields prevented opening existing libraries with custom entry types [#11127](https://github.com/JabRef/jabref/issues/11127)
+- We fixed an issue where Markdown rendering removed braces from the text. [#10928](https://github.com/JabRef/jabref/issues/10928)
 - We fixed an issue when the file was flagged as changed on disk in the case of content selectors or groups. [#9064](https://github.com/JabRef/jabref/issues/9064)
 - We fixed crash on opening the entry editor when auto completion is enabled. [#11188](https://github.com/JabRef/jabref/issues/11188)
 - We fixed the usage of the key binding for "Clear search" (default: <kbd>Escape</kbd>). [#10764](https://github.com/JabRef/jabref/issues/10764)
diff --git a/src/main/java/org/jabref/logic/layout/format/HTMLChars.java b/src/main/java/org/jabref/logic/layout/format/HTMLChars.java
index 5bfe60c7bd1..9776f49a504 100644
--- a/src/main/java/org/jabref/logic/layout/format/HTMLChars.java
+++ b/src/main/java/org/jabref/logic/layout/format/HTMLChars.java
@@ -4,14 +4,14 @@
 import java.util.Objects;
 import java.util.regex.Pattern;
 
-import org.jabref.logic.layout.LayoutFormatter;
+import org.jabref.logic.layout.ParamLayoutFormatter;
 import org.jabref.logic.util.strings.HTMLUnicodeConversionMaps;
 import org.jabref.model.strings.StringUtil;
 
 /**
- * This formatter escapes characters so they are suitable for HTML.
+ * This formatter escapes characters so that they are suitable for HTML.
  */
-public class HTMLChars implements LayoutFormatter {
+public class HTMLChars implements ParamLayoutFormatter {
 
     private static final Map<String, String> HTML_CHARS = HTMLUnicodeConversionMaps.LATEX_HTML_CONVERSION_MAP;
     /**
@@ -23,6 +23,15 @@ public class HTMLChars implements LayoutFormatter {
      * */
     private static final Pattern HTML_ENTITY_PATTERN = Pattern.compile("&(?!(?:[a-z0-9]+|#[0-9]{1,6}|#x[0-9a-fA-F]{1,6});)");
 
+    private boolean keepCurlyBraces = false;
+
+    @Override
+    public void setArgument(String arg) {
+        if ("keepCurlyBraces".equalsIgnoreCase(arg)) {
+            this.keepCurlyBraces = true;
+        }
+    }
+
     @Override
     public String format(String inField) {
         String field = normalizedField(inField);
@@ -49,7 +58,7 @@ public String format(String inField) {
                 escaped = true;
                 incommand = true;
                 currentCommand = new StringBuilder();
-            } else if (!incommand && ((c == '{') || (c == '}'))) {
+            } else if (!this.keepCurlyBraces && !incommand && ((c == '{') || (c == '}'))) {
                 // Swallow the brace.
             } else if (Character.isLetter(c) || StringUtil.SPECIAL_COMMAND_CHARS.contains(String.valueOf(c))) {
                 escaped = false;
@@ -73,7 +82,7 @@ public String format(String inField) {
                         String commandBody;
                         if (c == '{') {
                             String part = StringUtil.getPart(field, i, false);
-                            i += part.length();
+                            i += this.keepCurlyBraces ? part.length() + 1 : part.length();
                             commandBody = part;
                         } else {
                             commandBody = field.substring(i, i + 1);
@@ -83,7 +92,6 @@ public String format(String inField) {
                         sb.append(Objects.requireNonNullElse(result, commandBody));
 
                         incommand = false;
-                        escaped = false;
                     } else {
                         // Are we already at the end of the string?
                         if ((i + 1) == field.length()) {
@@ -109,11 +117,14 @@ public String format(String inField) {
                     String tag = getHTMLTag(command);
                     if (!tag.isEmpty()) {
                         String part = StringUtil.getPart(field, i, true);
+                        if (this.keepCurlyBraces && (c == '{' || (c == '}'))) {
+                            i++;
+                        }
                         i += part.length();
                         sb.append('<').append(tag).append('>').append(part).append("</").append(tag).append('>');
                     } else if (c == '{') {
                         String argument = StringUtil.getPart(field, i, true);
-                        i += argument.length();
+                        i += this.keepCurlyBraces ? argument.length() + 1 : argument.length();
                         // handle common case of general latex command
                         String result = HTML_CHARS.get(command + argument);
                         // If found, then use translated version. If not, then keep
@@ -133,10 +144,14 @@ public String format(String inField) {
                     } else if (c == '}') {
                         // This end brace terminates a command. This can be the case in
                         // constructs like {\aa}. The correct behaviour should be to
-                        // substitute the evaluated command and swallow the brace:
+                        // substitute the evaluated command.
                         String result = HTML_CHARS.get(command);
                         // If the command is unknown, just print it:
                         sb.append(Objects.requireNonNullElse(result, command));
+                        // We only keep the brace if we are in 'KEEP' mode.
+                        if (this.keepCurlyBraces) {
+                            sb.append(c);
+                        }
                     } else {
                         String result = HTML_CHARS.get(command);
                         sb.append(Objects.requireNonNullElse(result, command));
@@ -170,7 +185,7 @@ private String normalizedField(String inField) {
                                   .replaceAll("[\\n]{2,}", "<p>") // Replace double line breaks with <p>
                                   .replace("\n", "<br>") // Replace single line breaks with <br>
                                   .replace("\\$", "&dollar;") // Replace \$ with &dollar;
-                                  .replaceAll("\\$([^$]*)\\$", "\\{$1\\}");
+                                  .replaceAll("\\$([^$]*)\\$", this.keepCurlyBraces ? "\\\\{$1\\\\}" : "$1}");
     }
 
     private String getHTMLTag(String latexCommand) {
diff --git a/src/main/java/org/jabref/migrations/PreferencesMigrations.java b/src/main/java/org/jabref/migrations/PreferencesMigrations.java
index 92d60f49632..5a364ad06c5 100644
--- a/src/main/java/org/jabref/migrations/PreferencesMigrations.java
+++ b/src/main/java/org/jabref/migrations/PreferencesMigrations.java
@@ -331,6 +331,7 @@ protected static void upgradePreviewStyle(JabRefPreferences prefs) {
         String currentPreviewStyle = prefs.get(JabRefPreferences.PREVIEW_STYLE);
         String migratedStyle = currentPreviewStyle.replace("\\begin{review}<BR><BR><b>Review: </b> \\format[HTMLChars]{\\review} \\end{review}", "\\begin{comment}<BR><BR><b>Comment: </b> \\format[Markdown,HTMLChars]{\\comment} \\end{comment}")
                                                   .replace("\\format[HTMLChars]{\\comment}", "\\format[Markdown,HTMLChars]{\\comment}")
+                                                  .replace("\\format[Markdown,HTMLChars]{\\comment}", "\\format[Markdown,HTMLChars(keepCurlyBraces)]{\\comment}")
                                                   .replace("<b><i>\\bibtextype</i><a name=\"\\bibtexkey\">\\begin{bibtexkey} (\\bibtexkey)</a>", "<b><i>\\bibtextype</i><a name=\"\\citationkey\">\\begin{citationkey} (\\citationkey)</a>")
                                                   .replace("\\end{bibtexkey}</b><br>__NEWLINE__", "\\end{citationkey}</b><br>__NEWLINE__");
         prefs.put(JabRefPreferences.PREVIEW_STYLE, migratedStyle);
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index 55de7b43b54..d9c747b3a1e 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -821,7 +821,7 @@ private JabRefPreferences() {
                         "\\begin{pages}<BR> p. \\format[FormatPagesForHTML]{\\pages}\\end{pages}__NEWLINE__" +
                         "\\begin{abstract}<BR><BR><b>Abstract: </b>\\format[HTMLChars]{\\abstract} \\end{abstract}__NEWLINE__" +
                         "\\begin{owncitation}<BR><BR><b>Own citation: </b>\\format[HTMLChars]{\\owncitation} \\end{owncitation}__NEWLINE__" +
-                        "\\begin{comment}<BR><BR><b>Comment: </b>\\format[Markdown,HTMLChars]{\\comment}\\end{comment}__NEWLINE__" +
+                        "\\begin{comment}<BR><BR><b>Comment: </b>\\format[Markdown,HTMLChars(keepCurlyBraces)]{\\comment}\\end{comment}__NEWLINE__" +
                         "</font>__NEWLINE__");
 
         // set default theme
diff --git a/src/test/java/org/jabref/logic/layout/format/HTMLCharsTest.java b/src/test/java/org/jabref/logic/layout/format/HTMLCharsTest.java
index a31c04c7205..045ab4b5adf 100644
--- a/src/test/java/org/jabref/logic/layout/format/HTMLCharsTest.java
+++ b/src/test/java/org/jabref/logic/layout/format/HTMLCharsTest.java
@@ -3,6 +3,7 @@
 import java.util.stream.Stream;
 
 import org.jabref.logic.layout.LayoutFormatter;
+import org.jabref.logic.layout.ParamLayoutFormatter;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -15,10 +16,13 @@
 public class HTMLCharsTest {
 
     private LayoutFormatter layout;
+    private ParamLayoutFormatter layoutKeep;
 
     @BeforeEach
     public void setUp() {
         layout = new HTMLChars();
+        layoutKeep = new HTMLChars();
+        layoutKeep.setArgument("keepCurlyBraces");
     }
 
     private static Stream<Arguments> provideBasicFormattingData() {
@@ -37,6 +41,7 @@ private static Stream<Arguments> provideBasicFormattingData() {
                 Arguments.of("&auml;", "{\\\"a}"),
                 Arguments.of("&auml;", "\\\"a"),
                 Arguments.of("&Ccedil;", "{\\c{C}}"),
+                Arguments.of("&Ccedil;", "\\c{C}"),
                 Arguments.of("&Oogon;&imath;", "\\k{O}\\i"),
                 Arguments.of("&ntilde; &ntilde; &iacute; &imath; &imath;", "\\~{n} \\~n \\'i \\i \\i")
         );
@@ -144,4 +149,23 @@ private static Stream<Arguments> provideHTMLEntityFormattingData() {
     void hTMLEntityFormatting(String expected, String input) {
         assertEquals(expected, layout.format(input));
     }
+
+    private static Stream<Arguments> provideBracesKeepFormattingData() {
+        return Stream.of(
+            Arguments.of("{&auml;}", "{\\\"{a}}"),
+            Arguments.of("{&auml;}", "{\\\"a}"),
+            Arguments.of("{&Ccedil;}", "{\\c{C}}"),
+            Arguments.of("{<em>hallo</em>}", "{\\emph hallo}"),
+            Arguments.of("{<b>hallo</b>}", "{\\textbf hallo}"),
+            Arguments.of("{<b>hallo</b>}", "{\\bf hallo}"),
+            Arguments.of("{&#39;}", "{\\textquotesingle}"),
+            Arguments.of("{{ test }}", "{{ test }}")
+        );
+    }
+
+    @ParameterizedTest
+    @MethodSource("provideBracesKeepFormattingData")
+    void bracesKeepFormatting(String expected, String input) {
+        assertEquals(expected, layoutKeep.format(input));
+    }
 }
diff --git a/src/test/java/org/jabref/logic/layout/format/MarkdownFormatterTest.java b/src/test/java/org/jabref/logic/layout/format/MarkdownFormatterTest.java
index e5e1f9281e6..2bfb5ef4caa 100644
--- a/src/test/java/org/jabref/logic/layout/format/MarkdownFormatterTest.java
+++ b/src/test/java/org/jabref/logic/layout/format/MarkdownFormatterTest.java
@@ -1,10 +1,14 @@
 package org.jabref.logic.layout.format;
 
+import java.util.stream.Stream;
+
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
 class MarkdownFormatterTest {
@@ -17,23 +21,74 @@ void setUp() {
     }
 
     @Test
-    void formatWhenFormattingPlainTextThenReturnsTextWrappedInParagraph() {
-        assertEquals("<p>Hello World</p>", markdownFormatter.format("Hello World"));
-    }
-
-    @Test
-    void formatWhenFormattingComplexMarkupThenReturnsOnlyOneLine() {
-        assertFalse(markdownFormatter.format("Markup\n\n* list item one\n* list item 2\n\n rest").contains("\n"));
+    void formatWhenFormattingNullThenThrowsException() {
+        Exception exception = assertThrows(NullPointerException.class, () -> markdownFormatter.format(null));
+        assertEquals("Field Text should not be null, when handed to formatter", exception.getMessage());
     }
 
-    @Test
-    void formatWhenFormattingEmptyStringThenReturnsEmptyString() {
-        assertEquals("", markdownFormatter.format(""));
+    private static Stream<Arguments> provideMarkdownAndHtml() {
+        return Stream.of(
+                Arguments.of("Hello World", "<p>Hello World</p>"),
+                Arguments.of("""
+                        Markup
+                        
+                        * list item one
+                        * list item two
+                        
+                         rest
+                        """,
+                        "<p>Markup</p> <ul> <li>list item one</li> <li>list item two</li> </ul> <p>rest</p>"
+                ),
+                Arguments.of("""
+                        ```
+                        Hello World
+                        ```
+                        """,
+                        "<pre><code>Hello World </code></pre>"
+                ),
+                Arguments.of("""
+                       First line
+                    
+                       Second line
+                    
+                       ```java
+                       String test;
+                       ```
+                    """,
+                    "<p>First line</p> <p>Second line</p> <pre><code class=\"language-java\">String test; </code></pre>"
+                ),
+                Arguments.of("""
+                       Some text.
+                       ```javascript
+                       let test = "Hello World";
+                       ```
+                    
+                       ```java
+                       String test = "Hello World";
+                       ```
+                       Some more text.
+                    """,
+                    "<p>Some text.</p> <pre><code class=\"language-javascript\">let test = &quot;Hello World&quot;; " +
+                            "</code></pre> <pre><code class=\"language-java\">String test = &quot;Hello World&quot;; " +
+                            "</code></pre> <p>Some more text.</p>"
+                ),
+                Arguments.of("""
+                        Some text.
+                        
+                        ```java
+                        int foo = 0;
+                        foo = 1;
+                        
+                        ```
+                        """,
+                        "<p>Some text.</p> <pre><code class=\"language-java\">int foo = 0; foo = 1;  </code></pre>"
+                )
+        );
     }
 
-    @Test
-    void formatWhenFormattingNullThenThrowsException() {
-        Exception exception = assertThrows(NullPointerException.class, () -> markdownFormatter.format(null));
-        assertEquals("Field Text should not be null, when handed to formatter", exception.getMessage());
+    @ParameterizedTest
+    @MethodSource("provideMarkdownAndHtml")
+    void formatWhenFormattingCodeBlockThenReturnsCodeBlockInHtml(String markdown, String expectedHtml) {
+        assertEquals(expectedHtml, markdownFormatter.format(markdown));
     }
 }
diff --git a/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java b/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
index 0a89c471788..9b3f8f0c145 100644
--- a/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
+++ b/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
@@ -84,8 +84,8 @@ void previewStyleReviewToComment() {
 
         String newPreviewStyle = "<font face=\"sans-serif\">__NEWLINE__"
                 + "Customized preview style using reviews and comments:__NEWLINE__"
-                + "\\begin{comment}<BR><BR><b>Comment: </b> \\format[Markdown,HTMLChars]{\\comment} \\end{comment}__NEWLINE__"
-                + "\\begin{comment} Something: \\format[Markdown,HTMLChars]{\\comment} special \\end{comment}__NEWLINE__"
+                + "\\begin{comment}<BR><BR><b>Comment: </b> \\format[Markdown,HTMLChars(keepCurlyBraces)]{\\comment} \\end{comment}__NEWLINE__"
+                + "\\begin{comment} Something: \\format[Markdown,HTMLChars(keepCurlyBraces)]{\\comment} special \\end{comment}__NEWLINE__"
                 + "</font>__NEWLINE__";
 
         when(prefs.get(JabRefPreferences.PREVIEW_STYLE)).thenReturn(oldPreviewStyle);

From 073fbafa9b869949a7180430029b0e9854fdc204 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 23 Apr 2024 12:27:18 +0200
Subject: [PATCH 07/54] Update external-libraries.md (#11242)

---
 external-libraries.md | 50 +++++++++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 23 deletions(-)

diff --git a/external-libraries.md b/external-libraries.md
index 16b5165fe82..96695fdc1b7 100644
--- a/external-libraries.md
+++ b/external-libraries.md
@@ -691,9 +691,13 @@ License: BSD-3-Clause
 
 ## Sorted list of runtime dependencies output by gradle
 
-1. `./gradlew dependencies > build/dependencies.txt`
-2. Manually edit depedencies.txt to contain the tree of "compileClasspath" and "implementation" only. Otherwise, libraries such as "Apache Commons Lang 3" are missed. Ensure LF as line ending.
-3. (on WSL) `sed 's/[^a-z]*//' < build/dependencies.txt | sed "s/\(.*\) .*/\1/" | grep -v "\->" | sort | uniq > build/dependencies-for-external-libraries.txt`
+1. `./gradlew dependencyReport --configuration compileClasspath`
+2. Fix `build/reports/project/dependencies.txt`
+
+   - Change line endings to `LF`
+   - Remove text above and below the tree
+
+3. (on WSL) `sed 's/[^a-z]*//' < build/reports/project/dependencies.txt | sed "s/\(.*\) .*/\1/" | grep -v "\->" | sort | uniq > build/dependencies-for-external-libraries.txt`
 
 ```text
 at.favre.lib:hkdf:1.1.0
@@ -809,7 +813,7 @@ org.apache.pdfbox:fontbox:3.0.2
 org.apache.pdfbox:pdfbox-io:3.0.2
 org.apache.pdfbox:pdfbox:3.0.2
 org.apache.pdfbox:xmpbox:3.0.2
-org.bouncycastle:bcprov-jdk18on:1.77
+org.bouncycastle:bcprov-jdk18on:1.78
 org.checkerframework:checker-qual:3.42.0
 org.codehaus.woodstox:stax2-api:4.2
 org.controlsfx:controlsfx:11.2.1
@@ -818,24 +822,24 @@ org.fxmisc.flowless:flowless:0.7.2
 org.fxmisc.richtext:richtextfx:0.11.2
 org.fxmisc.undo:undofx:2.1.1
 org.fxmisc.wellbehaved:wellbehavedfx:0.3.3
-org.glassfish.grizzly:grizzly-framework:4.0.1
-org.glassfish.grizzly:grizzly-http-server:4.0.1
-org.glassfish.grizzly:grizzly-http:4.0.1
+org.glassfish.grizzly:grizzly-framework:4.0.2
+org.glassfish.grizzly:grizzly-http-server:4.0.2
+org.glassfish.grizzly:grizzly-http:4.0.2
 org.glassfish.hk2.external:aopalliance-repackaged:3.1.0
 org.glassfish.hk2:hk2-api:3.1.0
-org.glassfish.hk2:hk2-locator:3.0.5
+org.glassfish.hk2:hk2-locator:3.0.6
 org.glassfish.hk2:hk2-utils:3.1.0
 org.glassfish.hk2:osgi-resource-locator:1.0.3
 org.glassfish.jaxb:jaxb-core:4.0.3
 org.glassfish.jaxb:jaxb-runtime:4.0.3
 org.glassfish.jaxb:txw2:4.0.3
-org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.5
-org.glassfish.jersey.core:jersey-client:3.1.5
-org.glassfish.jersey.core:jersey-common:3.1.5
-org.glassfish.jersey.core:jersey-server:3.1.5
-org.glassfish.jersey.inject:jersey-hk2:3.1.5
+org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.6
+org.glassfish.jersey.core:jersey-client:3.1.6
+org.glassfish.jersey.core:jersey-common:3.1.6
+org.glassfish.jersey.core:jersey-server:3.1.6
+org.glassfish.jersey.inject:jersey-hk2:3.1.6
 org.jabref:afterburner.fx:2.0.0
-org.javassist:javassist:3.29.2-GA
+org.javassist:javassist:3.30.2-GA
 org.jbibtex:jbibtex:1.0.20
 org.jetbrains:annotations:24.0.1
 org.jooq:jool:0.9.15
@@ -850,18 +854,18 @@ org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1
 org.libreoffice:libreoffice:7.6.4
 org.libreoffice:unoloader:7.6.4
 org.mariadb.jdbc:mariadb-java-client:2.7.9
-org.openjfx:javafx-base:22
-org.openjfx:javafx-controls:22
-org.openjfx:javafx-fxml:22
-org.openjfx:javafx-graphics:22
-org.openjfx:javafx-media:22
-org.openjfx:javafx-swing:22
-org.openjfx:javafx-web:22
+org.openjfx:javafx-base:22.0.1
+org.openjfx:javafx-controls:22.0.1
+org.openjfx:javafx-fxml:22.0.1
+org.openjfx:javafx-graphics:22.0.1
+org.openjfx:javafx-media:22.0.1
+org.openjfx:javafx-swing:22.0.1
+org.openjfx:javafx-web:22.0.1
 org.postgresql:postgresql:42.7.3
 org.reactfx:reactfx:2.0-M5
 org.scala-lang:scala-library:2.13.8
-org.slf4j:jul-to-slf4j:2.0.12
-org.slf4j:slf4j-api:2.0.12
+org.slf4j:jul-to-slf4j:2.0.13
+org.slf4j:slf4j-api:2.0.13
 org.tinylog:slf4j-tinylog:2.7.0
 org.tinylog:tinylog-api:2.7.0
 org.tinylog:tinylog-impl:2.7.0

From 47dbcdb8caf97a5c455eb98337d74add38c74c5b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 23 Apr 2024 10:52:47 +0000
Subject: [PATCH 08/54] Bump com.dlsc.gemsfx:gemsfx from 2.8.0 to 2.9.0
 (#11239)

* Bump com.dlsc.gemsfx:gemsfx from 2.8.0 to 2.9.0

Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.8.0 to 2.9.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/CHANGELOG.md)
- [Commits](https://github.com/dlsc-software-consulting-gmbh/GemsFX/compare/v2.8.0...v2.9.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update transitive dependency

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
---
 build.gradle | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 76c0d2cefcb..0ebf42a254e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -218,12 +218,15 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.8.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.9.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.openjfx'
         exclude group: 'org.apache.logging.log4j'
+        exclude group: 'tech.units'
     }
+    // Required by gemsfx
+    implementation 'tech.units:indriya:2.2'
 
     implementation 'org.controlsfx:controlsfx:11.2.1'
 

From 91f956cca061ad33141a22c8ff3b08c7e145ed72 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 29 Apr 2024 08:46:27 +0200
Subject: [PATCH 09/54] Add check for PRs from "main" (#11252)

* Add check for PRs from "main"

* Fix workflow

* Try multiline message

* More emoji

* Reword
---
 .github/workflows/tests.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index fa4bc3f0276..34e34a5086c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -335,3 +335,12 @@ jobs:
           show-progress: 'false'
       - name: Merge Conflict finder
         uses: olivernybroe/action-conflict-finder@v4.0
+  other_than_main:
+    name: Source branch is other than "main"
+    runs-on: ubuntu-latest
+    steps:
+      - if: github.head_ref == 'main'
+        uses: actions/github-script@v6
+        with:
+          script: |
+              core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read https://devdocs.jabref.org/contributing again carefully. 👈')

From 70b7748fdd0696357d9bfd9f0fa5b994cb1e0c07 Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Mon, 29 Apr 2024 10:07:02 +0300
Subject: [PATCH 10/54] Add directory monitor for Latex citations (#11245)

* Add directory monitor

* Ignore parsing nested files

* Add listener for LaTex directory, update LatexCitationsTab

* Update CHANGELOG.md

* Decision record

* Refine ADR-030

* Update module-info.java

* handle non-existing directories

* Java Doc

* Java Doc

* Move directoryMonitor to Globals

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
---
 CHANGELOG.md                                  |   1 +
 build.gradle                                  |   2 +
 .../0028-http-return-bibtex-string.md         |   2 -
 .../0029-cff-export-multiple-entries.md       |   5 +-
 ...che-commons-io-for-directory-monitoring.md |  48 ++++
 external-libraries.md                         |  23 +-
 src/main/java/module-info.java                |  11 +-
 src/main/java/org/jabref/gui/Globals.java     |  15 ++
 src/main/java/org/jabref/gui/LibraryTab.java  |  16 +-
 .../java/org/jabref/gui/StateManager.java     |   2 +-
 .../jabref/gui/entryeditor/EntryEditor.java   |   5 +-
 .../gui/entryeditor/LatexCitationsTab.java    |  43 ++--
 .../LatexCitationsTabViewModel.java           | 213 ++++++++++++------
 .../gui/util/DefaultDirectoryMonitor.java     |  54 +++++
 .../logic/texparser/CitationFinder.java       |  56 -----
 .../logic/texparser/DefaultLatexParser.java   |  25 +-
 .../model/texparser/LatexParserResults.java   |  23 +-
 .../jabref/model/util/DirectoryMonitor.java   |  25 ++
 .../model/util/DirectoryMonitorManager.java   |  36 +++
 src/main/resources/l10n/JabRef_en.properties  |   2 +-
 20 files changed, 412 insertions(+), 195 deletions(-)
 create mode 100644 docs/decisions/0030-use-apache-commons-io-for-directory-monitoring.md
 create mode 100644 src/main/java/org/jabref/gui/util/DefaultDirectoryMonitor.java
 delete mode 100644 src/main/java/org/jabref/logic/texparser/CitationFinder.java
 create mode 100644 src/main/java/org/jabref/model/util/DirectoryMonitor.java
 create mode 100644 src/main/java/org/jabref/model/util/DirectoryMonitorManager.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99fc9dfa8fa..134ec7736be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added tooltip on main table cells that shows cell content or cell content and entry preview if set in preferences. [10925](https://github.com/JabRef/jabref/issues/10925)
 - We added the ability to add a keyword/crossref when typing the separator character (e.g., comma) in the keywords/crossref fields. [#11178](https://github.com/JabRef/jabref/issues/11178)
 - We added an exporter and improved the importer for Endnote XML format. [#11137](https://github.com/JabRef/jabref/issues/11137)
+- We added support for automatically update LaTeX citations when a LaTeX file is created, removed, or modified. [#10585](https://github.com/JabRef/jabref/issues/10585)
 
 ### Changed
 
diff --git a/build.gradle b/build.gradle
index 0ebf42a254e..28db2f20df6 100644
--- a/build.gradle
+++ b/build.gradle
@@ -296,6 +296,8 @@ dependencies {
     // YAML formatting
     implementation 'org.yaml:snakeyaml:2.2'
 
+    implementation 'commons-io:commons-io:2.16.1'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.170'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
diff --git a/docs/decisions/0028-http-return-bibtex-string.md b/docs/decisions/0028-http-return-bibtex-string.md
index e60a931d54a..bc8ff9394eb 100644
--- a/docs/decisions/0028-http-return-bibtex-string.md
+++ b/docs/decisions/0028-http-return-bibtex-string.md
@@ -2,8 +2,6 @@
 nav_order: 28
 parent: Decision Records
 ---
-<!-- we need to disable MD025, because we use the different heading "ADR Template" in the homepage (see above) than it is foreseen in the template -->
-<!-- markdownlint-disable-next-line MD025 -->
 # Return BibTeX string and CSL Item JSON in the API
 
 ## Context and Problem Statement
diff --git a/docs/decisions/0029-cff-export-multiple-entries.md b/docs/decisions/0029-cff-export-multiple-entries.md
index 179ceab745d..ec1dab8cfc0 100644
--- a/docs/decisions/0029-cff-export-multiple-entries.md
+++ b/docs/decisions/0029-cff-export-multiple-entries.md
@@ -1,10 +1,7 @@
 ---
-nav_order: 28
+nav_order: 29
 parent: Decision Records
 ---
-
-<!-- we need to disable MD025, because we use the different heading "ADR Template" in the homepage (see above) than it is foreseen in the template -->
-<!-- markdownlint-disable-next-line MD025 -->
 # Exporting multiple entries to CFF
 
 ## Context and Problem Statement
diff --git a/docs/decisions/0030-use-apache-commons-io-for-directory-monitoring.md b/docs/decisions/0030-use-apache-commons-io-for-directory-monitoring.md
new file mode 100644
index 00000000000..42a762132c8
--- /dev/null
+++ b/docs/decisions/0030-use-apache-commons-io-for-directory-monitoring.md
@@ -0,0 +1,48 @@
+---
+nav_order: 30
+parent: Decision Records
+---
+# Use Apache Commons IO for directory monitoring
+
+## Context and Problem Statement
+
+In JabRef, there is a need to add a directory monitor that will listen for changes in a specified directory.
+
+Currently, the monitor is used to automatically update the [LaTeX Citations](https://docs.jabref.org/advanced/entryeditor/latex-citations) when a LaTeX file in the LaTeX directory is created, removed, or modified ([#10585](https://github.com/JabRef/jabref/issues/10585)).
+Additionally, this monitor will be used to create a dynamic group that mirrors the file system structure ([#10930](https://github.com/JabRef/jabref/issues/10930)).
+
+## Considered Options
+
+* Use [java.nio.file.WatchService](https://docs.oracle.com/en/java/javase/22/docs/api/java.base/java/nio/file/WatchService.html)
+* Use [io.methvin.watcher.DirectoryWatcher](https://github.com/gmethvin/directory-watcher)
+* Use [org.apache.commons.io.monitor](https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/monitor/package-summary.html)
+
+## Decision Outcome
+
+Chosen option: "Use [org.apache.commons.io.monitor](https://commons.apache.org/proper/commons-io/apidocs/org/apache/commons/io/monitor/package-summary.html)", because comes out best (see below).
+
+## Pros and Cons of the Options
+
+### java.nio.file.WatchService
+
+* Good, because it is a standard Java API for watching directories.
+* Good, because it does not need polling, it is event-based for most operating systems.
+* Bad, because:
+  1. Does not detect files coming together with a new folder (JDK issue: [JDK-8162948](https://bugs.openjdk.org/browse/JDK-8162948)).
+  2. Deleting a subdirectory does not detect deleted files in that directory.
+  3. Access denied when trying to delete the recursively watched directory on Windows (JDK issue: [JDK-6972833](https://bugs.openjdk.org/browse/JDK-6972833)).
+  4. Implemented on macOS by the generic `PollingWatchService`. (JDK issue: [JDK-8293067](https://bugs.openjdk.org/browse/JDK-8293067))
+
+### io.methvin.watcher.DirectoryWatcher
+
+* Good, because it implemented on top of the `java.nio.file.WatchService`, which is a standard Java API for watching directories.
+* Good, because it resolves some of the issues of the `java.nio.file.WatchService`.
+  * Uses`ExtendedWatchEventModifier.FILE_TREE` on Windows, which resolves issues (1, 3) of the `java.nio.file.WatchService`.
+  * On macOS have native implementation based on the Carbon File System Events API, this resolves issue (4) of the `java.nio.file.WatchService`.
+* Bad, because issue (2) of the `java.nio.file.WatchService` is not resolved.
+
+### org.apache.commons.io.monitor
+
+* Good, because there are no observed issues.
+* Good, because can handle huge amount of files without overflowing.
+* Bad, because it uses a polling mechanism at fixed intervals, which can waste CPU cycles if no change occurs.
diff --git a/external-libraries.md b/external-libraries.md
index 96695fdc1b7..a4e483bb84d 100644
--- a/external-libraries.md
+++ b/external-libraries.md
@@ -294,6 +294,12 @@ Project: Apache Commons Digester
 URL:     https://commons.apache.org/proper/commons-digester/
 ```
 
+```yaml
+Id:      commons-io:commons-io
+Project: Apache Commons IO
+URL:     https://commons.apache.org/proper/commons-io/
+```
+
 ```yaml
 Id:      de.rototor.jeuclid:jeuclid-core
 Project: JEuclid
@@ -537,7 +543,7 @@ Id:      com.ibm.icu:*
 Project: International Components for Unicode
 URL:     https://icu.unicode.org/
 License: Unicode License (https://www.unicode.org/copyright.html)
-Note:    Our own fork https://github.com/JabRef/icu. Upstream PR: https://github.com/unicode-org/icu/pull/2127
+Note:    Our own fork https://github.com/JabRef/icu. [Upstream PR](https://github.com/unicode-org/icu/pull/2127)
 Path:    lib/icu4j.jar
 SourcePath: lib/ic4j-src.jar
 ```
@@ -579,49 +585,49 @@ License: LGPL-2.1-or-later
 
 ```yaml
 Id:      org.openjfx:javafx-base
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-controls
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-fxml
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-graphics
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-media
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-swing
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
 
 ```yaml
 Id:      org.openjfx:javafx-web
-Project  JavaFX
+Project: JavaFX
 URL:     https://openjfx.io/
 License: GPL-2.0 WITH Classpath-exception-2.0
 ```
@@ -765,6 +771,7 @@ commons-cli:commons-cli:1.6.0
 commons-codec:commons-codec:1.16.0
 commons-collections:commons-collections:3.2.2
 commons-digester:commons-digester:2.1
+commons-io:commons-io:2.16.1
 commons-logging:commons-logging:1.2
 commons-validator:commons-validator:1.7
 de.rototor.jeuclid:jeuclid-core:3.1.11
diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
index 597270bf308..352ef69c95b 100644
--- a/src/main/java/module-info.java
+++ b/src/main/java/module-info.java
@@ -54,6 +54,9 @@
     requires java.prefs;
     requires com.fasterxml.aalto;
 
+    // YAML
+    requires org.yaml.snakeyaml;
+
     // Annotations (@PostConstruct)
     requires jakarta.annotation;
     requires jakarta.inject;
@@ -88,13 +91,14 @@
     uses org.mariadb.jdbc.credential.CredentialPlugin;
 
     // Apache Commons and other (similar) helper libraries
+    requires com.google.common;
+    requires io.github.javadiffutils;
+    requires java.string.similarity;
     requires org.apache.commons.cli;
     requires org.apache.commons.csv;
+    requires org.apache.commons.io;
     requires org.apache.commons.lang3;
     requires org.apache.commons.text;
-    requires com.google.common;
-    requires io.github.javadiffutils;
-    requires java.string.similarity;
 
     requires com.github.tomtung.latex2unicode;
     requires fastparse;
@@ -146,5 +150,4 @@
     requires de.saxsys.mvvmfx.validation;
     requires dd.plist;
     requires mslinks;
-    requires org.yaml.snakeyaml;
 }
diff --git a/src/main/java/org/jabref/gui/Globals.java b/src/main/java/org/jabref/gui/Globals.java
index 4bbb5dbb2d8..bb8a45f8d8b 100644
--- a/src/main/java/org/jabref/gui/Globals.java
+++ b/src/main/java/org/jabref/gui/Globals.java
@@ -5,6 +5,7 @@
 import org.jabref.gui.remote.CLIMessageHandler;
 import org.jabref.gui.telemetry.Telemetry;
 import org.jabref.gui.undo.CountingUndoManager;
+import org.jabref.gui.util.DefaultDirectoryMonitor;
 import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
@@ -14,6 +15,7 @@
 import org.jabref.logic.remote.server.RemoteListenerServerManager;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.util.DirectoryMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
@@ -65,6 +67,7 @@ public class Globals {
     private static KeyBindingRepository keyBindingRepository;
 
     private static DefaultFileUpdateMonitor fileUpdateMonitor;
+    private static DefaultDirectoryMonitor directoryMonitor;
 
     private Globals() {
     }
@@ -92,6 +95,13 @@ public static synchronized FileUpdateMonitor getFileUpdateMonitor() {
         return fileUpdateMonitor;
     }
 
+    public static DirectoryMonitor getDirectoryMonitor() {
+        if (directoryMonitor == null) {
+            directoryMonitor = new DefaultDirectoryMonitor();
+        }
+        return directoryMonitor;
+    }
+
     // Background tasks
     public static void startBackgroundTasks() {
         // TODO Currently deactivated due to incompatibilities in XML
@@ -109,6 +119,11 @@ public static void shutdownThreadPools() {
         if (fileUpdateMonitor != null) {
             fileUpdateMonitor.shutdown();
         }
+
+        if (directoryMonitor != null) {
+            directoryMonitor.shutdown();
+        }
+
         JabRefExecutorService.INSTANCE.shutdownEverything();
     }
 
diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
index 48231b2f967..02ee691c747 100644
--- a/src/main/java/org/jabref/gui/LibraryTab.java
+++ b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -84,6 +84,7 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
 import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.util.DirectoryMonitorManager;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
@@ -127,9 +128,9 @@ private enum PanelMode { MAIN_TABLE, MAIN_TABLE_AND_ENTRY_EDITOR }
 
     // Indicates whether the tab is loading data using a dataloading task
     // The constructors take care to the right true/false assignment during start.
-    private SimpleBooleanProperty loading = new SimpleBooleanProperty(false);
+    private final SimpleBooleanProperty loading = new SimpleBooleanProperty(false);
 
-    // initally, the dialog is loading, not saving
+    // initially, the dialog is loading, not saving
     private boolean saving = false;
 
     private PersonNameSuggestionProvider searchAutoCompleter;
@@ -151,6 +152,7 @@ private enum PanelMode { MAIN_TABLE, MAIN_TABLE_AND_ENTRY_EDITOR }
 
     private final IndexingTaskManager indexingTaskManager;
     private final TaskExecutor taskExecutor;
+    private final DirectoryMonitorManager directoryMonitorManager;
 
     private LibraryTab(BibDatabaseContext bibDatabaseContext,
                       LibraryTabContainer tabContainer,
@@ -171,6 +173,7 @@ private LibraryTab(BibDatabaseContext bibDatabaseContext,
         this.entryTypesManager = entryTypesManager;
         this.indexingTaskManager = new IndexingTaskManager(taskExecutor);
         this.taskExecutor = taskExecutor;
+        this.directoryMonitorManager = new DirectoryMonitorManager(Globals.getDirectoryMonitor());
 
         bibDatabaseContext.getDatabase().registerListener(this);
         bibDatabaseContext.getMetaData().registerListener(this);
@@ -832,6 +835,11 @@ private void onClosed(Event event) {
         } catch (RuntimeException e) {
             LOGGER.error("Problem when closing change monitor", e);
         }
+        try {
+            directoryMonitorManager.unregister();
+        } catch (RuntimeException e) {
+            LOGGER.error("Problem when closing directory monitor", e);
+        }
         try {
             PdfIndexerManager.shutdownIndexer(bibDatabaseContext);
         } catch (RuntimeException e) {
@@ -864,6 +872,10 @@ public BibDatabaseContext getBibDatabaseContext() {
         return this.bibDatabaseContext;
     }
 
+    public DirectoryMonitorManager getDirectoryMonitorManager() {
+        return directoryMonitorManager;
+    }
+
     public boolean isSaving() {
         return saving;
     }
diff --git a/src/main/java/org/jabref/gui/StateManager.java b/src/main/java/org/jabref/gui/StateManager.java
index 2c842cd213d..010375fc1c5 100644
--- a/src/main/java/org/jabref/gui/StateManager.java
+++ b/src/main/java/org/jabref/gui/StateManager.java
@@ -190,7 +190,7 @@ public ObservableList<Task<?>> getBackgroundTasks() {
     }
 
     public void addBackgroundTask(BackgroundTask<?> backgroundTask, Task<?> task) {
-        this.backgroundTasks.add(0, new Pair<>(backgroundTask, task));
+        this.backgroundTasks.addFirst(new Pair<>(backgroundTask, task));
     }
 
     public EasyBinding<Boolean> getAnyTaskRunning() {
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index e2621d4cec0..220d11e2299 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -55,6 +55,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.Field;
+import org.jabref.model.util.DirectoryMonitorManager;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
@@ -82,6 +83,7 @@ public class EntryEditor extends BorderPane {
     private final BibDatabaseContext databaseContext;
     private final EntryEditorPreferences entryEditorPreferences;
     private final ExternalFilesEntryLinker fileLinker;
+    private final DirectoryMonitorManager directoryMonitorManager;
 
     private Subscription typeSubscription;
 
@@ -121,6 +123,7 @@ public class EntryEditor extends BorderPane {
     public EntryEditor(LibraryTab libraryTab) {
         this.libraryTab = libraryTab;
         this.databaseContext = libraryTab.getBibDatabaseContext();
+        this.directoryMonitorManager = libraryTab.getDirectoryMonitorManager();
 
         ViewLoader.view(this)
                   .root(this)
@@ -307,7 +310,7 @@ private List<EntryEditorTab> createTabs() {
                 bibEntryTypesManager,
                 keyBindingRepository);
         entryEditorTabs.add(sourceTab);
-        entryEditorTabs.add(new LatexCitationsTab(databaseContext, preferencesService, taskExecutor, dialogService));
+        entryEditorTabs.add(new LatexCitationsTab(databaseContext, preferencesService, dialogService, directoryMonitorManager));
         entryEditorTabs.add(new FulltextSearchResultsTab(stateManager, preferencesService, dialogService, taskExecutor));
 
         return entryEditorTabs;
diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTab.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTab.java
index 2272316bb8f..0be86194c87 100644
--- a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTab.java
@@ -17,10 +17,10 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.texparser.CitationsDisplay;
-import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.util.DirectoryMonitorManager;
 import org.jabref.preferences.PreferencesService;
 
 import com.tobiasdiez.easybind.EasyBind;
@@ -33,9 +33,17 @@ public class LatexCitationsTab extends EntryEditorTab {
     private final ProgressIndicator progressIndicator;
     private final CitationsDisplay citationsDisplay;
 
-    public LatexCitationsTab(BibDatabaseContext databaseContext, PreferencesService preferencesService,
-                             TaskExecutor taskExecutor, DialogService dialogService) {
-        this.viewModel = new LatexCitationsTabViewModel(databaseContext, preferencesService, taskExecutor, dialogService);
+    public LatexCitationsTab(BibDatabaseContext databaseContext,
+                             PreferencesService preferencesService,
+                             DialogService dialogService,
+                             DirectoryMonitorManager directoryMonitorManager) {
+
+        this.viewModel = new LatexCitationsTabViewModel(
+                databaseContext,
+                preferencesService,
+                dialogService,
+                directoryMonitorManager);
+
         this.searchPane = new GridPane();
         this.progressIndicator = new ProgressIndicator();
         this.citationsDisplay = new CitationsDisplay();
@@ -66,6 +74,11 @@ private void setSearchPane() {
         searchPane.setId("citationsPane");
         setContent(searchPane);
 
+        HBox latexDirectoryBox = getLatexDirectoryBox();
+        VBox citationsPane = getCitationsPane();
+        VBox notFoundPane = getNotFoundPane();
+        VBox errorPane = getErrorPane();
+
         EasyBind.subscribe(viewModel.statusProperty(), status -> {
             searchPane.getChildren().clear();
             switch (status) {
@@ -73,36 +86,35 @@ private void setSearchPane() {
                     searchPane.add(progressIndicator, 0, 0);
                     break;
                 case CITATIONS_FOUND:
-                    searchPane.add(getCitationsPane(), 0, 0);
+                    searchPane.add(citationsPane, 0, 0);
                     break;
                 case NO_RESULTS:
-                    searchPane.add(getNotFoundPane(), 0, 0);
+                    searchPane.add(notFoundPane, 0, 0);
                     break;
                 case ERROR:
-                    searchPane.add(getErrorPane(), 0, 0);
+                    searchPane.add(errorPane, 0, 0);
                     break;
             }
-            searchPane.add(getLatexDirectoryBox(), 0, 1);
+            searchPane.add(latexDirectoryBox, 0, 1);
         });
     }
 
     private HBox getLatexDirectoryBox() {
         Text latexDirectoryText = new Text(Localization.lang("Current search directory:"));
-        Text latexDirectoryPath = new Text(viewModel.directoryProperty().get().toString());
+        Text latexDirectoryPath = new Text();
+        latexDirectoryPath.textProperty().bind(viewModel.directoryProperty().asString());
         latexDirectoryPath.setStyle("-fx-font-family:monospace;-fx-font-weight: bold;");
         Button latexDirectoryButton = new Button(Localization.lang("Set LaTeX file directory"));
         latexDirectoryButton.setGraphic(IconTheme.JabRefIcons.LATEX_FILE_DIRECTORY.getGraphicNode());
         latexDirectoryButton.setOnAction(event -> viewModel.setLatexDirectory());
-        Button latexDirectoryRefreshButton = new Button(Localization.lang("Refresh"));
-        latexDirectoryRefreshButton.setGraphic(IconTheme.JabRefIcons.REFRESH.getGraphicNode());
-        latexDirectoryRefreshButton.setOnAction(event -> viewModel.refreshLatexDirectory());
-        HBox latexDirectoryBox = new HBox(10, latexDirectoryText, latexDirectoryPath, latexDirectoryButton, latexDirectoryRefreshButton);
+        HBox latexDirectoryBox = new HBox(10, latexDirectoryText, latexDirectoryPath, latexDirectoryButton);
         latexDirectoryBox.setAlignment(Pos.CENTER);
         return latexDirectoryBox;
     }
 
     private VBox getCitationsPane() {
         VBox citationsBox = new VBox(30, citationsDisplay);
+        VBox.setVgrow(citationsDisplay, Priority.ALWAYS);
         citationsBox.setStyle("-fx-padding: 0;");
         return citationsBox;
     }
@@ -122,7 +134,8 @@ private VBox getNotFoundPane() {
     private VBox getErrorPane() {
         Label titleLabel = new Label(Localization.lang("Error"));
         titleLabel.setStyle("-fx-font-size: 1.5em;-fx-font-weight: bold;-fx-text-fill: -fx-accent;");
-        Text errorMessageText = new Text(viewModel.searchErrorProperty().get());
+        Text errorMessageText = new Text();
+        errorMessageText.textProperty().bind(viewModel.searchErrorProperty());
         VBox errorMessageBox = new VBox(30, titleLabel, errorMessageText);
         errorMessageBox.setStyle("-fx-padding: 30 0 0 30;");
         return errorMessageBox;
@@ -130,7 +143,7 @@ private VBox getErrorPane() {
 
     @Override
     protected void bindToEntry(BibEntry entry) {
-        viewModel.init(entry);
+        viewModel.bindToEntry(entry);
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
index 833ce40ef63..2549e9ec211 100644
--- a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
@@ -1,11 +1,15 @@
 package org.jabref.gui.entryeditor;
 
+import java.io.File;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Collection;
 import java.util.Optional;
-import java.util.concurrent.Future;
 
+import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.ReadOnlyListWrapper;
+import javafx.beans.property.SimpleBooleanProperty;
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
@@ -14,23 +18,29 @@
 
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.DialogService;
-import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
-import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.texparser.CitationFinder;
+import org.jabref.logic.texparser.DefaultLatexParser;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.texparser.Citation;
+import org.jabref.model.texparser.LatexParserResult;
+import org.jabref.model.texparser.LatexParserResults;
+import org.jabref.model.util.DirectoryMonitorManager;
 import org.jabref.preferences.PreferencesService;
 
+import org.apache.commons.io.filefilter.FileFilterUtils;
+import org.apache.commons.io.filefilter.IOFileFilter;
+import org.apache.commons.io.monitor.FileAlterationListener;
+import org.apache.commons.io.monitor.FileAlterationObserver;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 public class LatexCitationsTabViewModel extends AbstractViewModel {
 
-    enum Status {
+    public enum Status {
         IN_PROGRESS,
         CITATIONS_FOUND,
         NO_RESULTS,
@@ -39,114 +49,187 @@ enum Status {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LatexCitationsTabViewModel.class);
     private static final String TEX_EXT = ".tex";
+    private static final IOFileFilter FILE_FILTER = FileFilterUtils.or(FileFilterUtils.suffixFileFilter(TEX_EXT), FileFilterUtils.directoryFileFilter());
     private final BibDatabaseContext databaseContext;
     private final PreferencesService preferencesService;
-    private final TaskExecutor taskExecutor;
     private final DialogService dialogService;
     private final ObjectProperty<Path> directory;
-    private CitationFinder citationFinder;
     private final ObservableList<Citation> citationList;
     private final ObjectProperty<Status> status;
     private final StringProperty searchError;
-    private Future<?> searchTask;
+    private final BooleanProperty updateStatusOnCreate;
+    private final DefaultLatexParser latexParser;
+    private final LatexParserResults latexFiles;
+    private final DirectoryMonitorManager directoryMonitorManager;
+    private final FileAlterationListener listener;
+    private FileAlterationObserver observer;
     private BibEntry currentEntry;
 
     public LatexCitationsTabViewModel(BibDatabaseContext databaseContext,
                                       PreferencesService preferencesService,
-                                      TaskExecutor taskExecutor,
-                                      DialogService dialogService) {
+                                      DialogService dialogService,
+                                      DirectoryMonitorManager directoryMonitorManager) {
+
         this.databaseContext = databaseContext;
         this.preferencesService = preferencesService;
-        this.taskExecutor = taskExecutor;
         this.dialogService = dialogService;
         this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getFilePreferences().getUserAndHost())
                                                                    .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService.getFilePreferences().getWorkingDirectory())));
 
-        this.citationFinder = new CitationFinder(directory.get());
         this.citationList = FXCollections.observableArrayList();
         this.status = new SimpleObjectProperty<>(Status.IN_PROGRESS);
         this.searchError = new SimpleStringProperty("");
+        this.directoryMonitorManager = directoryMonitorManager;
+        this.updateStatusOnCreate = new SimpleBooleanProperty(false);
+        this.listener = getListener();
+
+        this.latexParser = new DefaultLatexParser();
+        this.latexFiles = new LatexParserResults();
     }
 
-    public void init(BibEntry entry) {
-        cancelSearch();
+    private FileAlterationListener getListener() {
+        return new FileAlterationListener() {
+            @Override
+            public void onStart(FileAlterationObserver observer) {
+                if (!updateStatusOnCreate.get()) {
+                    status.set(Status.IN_PROGRESS);
+                }
+            }
+
+            @Override
+            public void onStop(FileAlterationObserver observer) {
+                if (!updateStatusOnCreate.get()) {
+                    updateStatusOnCreate.set(true);
+                    updateStatus();
+                }
+            }
+
+            @Override
+            public void onFileCreate(File file) {
+                Path path = file.toPath();
+                LatexParserResult result = latexParser.parse(path).get();
+                latexFiles.add(path, result);
+
+                Optional<String> citationKey = currentEntry.getCitationKey();
+                if (citationKey.isPresent()) {
+                    Collection<Citation> citations = result.getCitationsByKey(citationKey.get());
+                    DefaultTaskExecutor.runInJavaFXThread(() -> citationList.addAll(citations));
+                }
+
+                if (updateStatusOnCreate.get()) {
+                    updateStatus();
+                }
+            }
+
+            @Override
+            public void onFileDelete(File file) {
+                LatexParserResult result = latexFiles.remove(file.toPath());
+
+                Optional<String> citationKey = currentEntry.getCitationKey();
+                if (citationKey.isPresent()) {
+                    Collection<Citation> citations = result.getCitationsByKey(citationKey.get());
+                    DefaultTaskExecutor.runInJavaFXThread(() -> citationList.removeAll(citations));
+                    updateStatus();
+                }
+            }
+
+            @Override
+            public void onFileChange(File file) {
+                onFileDelete(file);
+                onFileCreate(file);
+                updateStatus();
+            }
+
+            @Override
+            public void onDirectoryChange(File directory) {
+            }
+
+            @Override
+            public void onDirectoryCreate(File directory) {
+            }
+
+            @Override
+            public void onDirectoryDelete(File directory) {
+            }
+        };
+    }
+
+    public void bindToEntry(BibEntry entry) {
+        checkAndUpdateDirectory();
 
         currentEntry = entry;
-        Optional<String> citeKey = entry.getCitationKey();
+        Optional<String> citationKey = entry.getCitationKey();
+
+        if (observer == null) {
+            observer = new FileAlterationObserver(directory.get().toFile(), FILE_FILTER);
+            directoryMonitorManager.addObserver(observer, listener);
+        }
 
-        if (citeKey.isPresent()) {
-            startSearch(citeKey.get());
+        if (citationKey.isPresent()) {
+            citationList.setAll(latexFiles.getCitationsByKey(citationKey.get()));
+            if (!status.get().equals(Status.IN_PROGRESS)) {
+                updateStatus();
+            }
         } else {
             searchError.set(Localization.lang("Selected entry does not have an associated citation key."));
             status.set(Status.ERROR);
         }
     }
 
-    public ObjectProperty<Path> directoryProperty() {
-        return directory;
-    }
-
-    public ObservableList<Citation> getCitationList() {
-        return new ReadOnlyListWrapper<>(citationList);
-    }
-
-    public ObjectProperty<Status> statusProperty() {
-        return status;
-    }
+    public void setLatexDirectory() {
+        DirectoryDialogConfiguration directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
+                .withInitialDirectory(directory.get()).build();
 
-    public StringProperty searchErrorProperty() {
-        return searchError;
-    }
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
+                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getFilePreferences().getUserAndHost(), selectedDirectory.toAbsolutePath()));
 
-    private void startSearch(String citeKey) {
-        // we need to check whether the user meanwhile set the LaTeX file directory or the database changed locations
         checkAndUpdateDirectory();
-
-        searchTask = BackgroundTask.wrap(() -> citationFinder.searchAndParse(citeKey))
-                                   .onRunning(() -> status.set(Status.IN_PROGRESS))
-                                   .onSuccess(result -> {
-                                       citationList.setAll(result);
-                                       status.set(citationList.isEmpty() ? Status.NO_RESULTS : Status.CITATIONS_FOUND);
-                                   })
-                                   .onFailure(error -> {
-                                       searchError.set(error.getMessage());
-                                       status.set(Status.ERROR);
-                                   })
-                                   .executeWith(taskExecutor);
-    }
-
-    private void cancelSearch() {
-        if (searchTask == null || searchTask.isCancelled() || searchTask.isDone()) {
-            return;
-        }
-
-        status.set(Status.IN_PROGRESS);
-        searchTask.cancel(true);
     }
 
-    public void checkAndUpdateDirectory() {
+    private void checkAndUpdateDirectory() {
         Path newDirectory = databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getFilePreferences().getUserAndHost())
                                            .orElse(FileUtil.getInitialDirectory(databaseContext, preferencesService.getFilePreferences().getWorkingDirectory()));
 
         if (!newDirectory.equals(directory.get())) {
+            status.set(Status.IN_PROGRESS);
+            updateStatusOnCreate.set(false);
+            citationList.clear();
+            latexFiles.clear();
+
+            directoryMonitorManager.removeObserver(observer);
             directory.set(newDirectory);
-            citationFinder = new CitationFinder(newDirectory);
+            observer = new FileAlterationObserver(directory.get().toFile(), FILE_FILTER);
+            directoryMonitorManager.addObserver(observer, listener);
         }
     }
 
-    public void setLatexDirectory() {
-        DirectoryDialogConfiguration directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                .withInitialDirectory(directory.get()).build();
+    private void updateStatus() {
+        DefaultTaskExecutor.runInJavaFXThread(() -> {
+            if (!Files.exists(directory.get())) {
+                searchError.set(Localization.lang("Current search directory does not exist: %0", directory.get()));
+                status.set(Status.ERROR);
+            } else if (citationList.isEmpty()) {
+                status.set(Status.NO_RESULTS);
+            } else {
+                status.set(Status.CITATIONS_FOUND);
+            }
+        });
+    }
 
-        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
-                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getFilePreferences().getUserAndHost(), selectedDirectory.toAbsolutePath()));
+    public ObjectProperty<Path> directoryProperty() {
+        return directory;
+    }
+
+    public ObservableList<Citation> getCitationList() {
+        return new ReadOnlyListWrapper<>(citationList);
+    }
 
-        init(currentEntry);
+    public ObjectProperty<Status> statusProperty() {
+        return status;
     }
 
-    public void refreshLatexDirectory() {
-        citationFinder = new CitationFinder(directory.get());
-        init(currentEntry);
+    public StringProperty searchErrorProperty() {
+        return searchError;
     }
 
     public boolean shouldShow() {
diff --git a/src/main/java/org/jabref/gui/util/DefaultDirectoryMonitor.java b/src/main/java/org/jabref/gui/util/DefaultDirectoryMonitor.java
new file mode 100644
index 00000000000..522a63632b0
--- /dev/null
+++ b/src/main/java/org/jabref/gui/util/DefaultDirectoryMonitor.java
@@ -0,0 +1,54 @@
+package org.jabref.gui.util;
+
+import org.jabref.model.util.DirectoryMonitor;
+
+import org.apache.commons.io.monitor.FileAlterationListener;
+import org.apache.commons.io.monitor.FileAlterationMonitor;
+import org.apache.commons.io.monitor.FileAlterationObserver;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class DefaultDirectoryMonitor implements DirectoryMonitor {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(DefaultDirectoryMonitor.class);
+    private static final int POLL_INTERVAL = 1000;
+
+    private final FileAlterationMonitor monitor;
+
+    public DefaultDirectoryMonitor() {
+        monitor = new FileAlterationMonitor(POLL_INTERVAL);
+        start();
+    }
+
+    @Override
+    public void addObserver(FileAlterationObserver observer, FileAlterationListener listener) {
+        if (observer != null) {
+            observer.addListener(listener);
+            monitor.addObserver(observer);
+        }
+    }
+
+    @Override
+    public void removeObserver(FileAlterationObserver observer) {
+        if (observer != null) {
+            monitor.removeObserver(observer);
+        }
+    }
+
+    public void start() {
+        try {
+            monitor.start();
+        } catch (Exception e) {
+            LOGGER.error("Error starting directory monitor", e);
+        }
+    }
+
+    @Override
+    public void shutdown() {
+        try {
+            monitor.stop();
+        } catch (Exception e) {
+            LOGGER.error("Error stopping directory monitor", e);
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/logic/texparser/CitationFinder.java b/src/main/java/org/jabref/logic/texparser/CitationFinder.java
deleted file mode 100644
index fac31569876..00000000000
--- a/src/main/java/org/jabref/logic/texparser/CitationFinder.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.jabref.logic.texparser;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.Collection;
-import java.util.List;
-import java.util.stream.Stream;
-
-import org.jabref.model.texparser.Citation;
-import org.jabref.model.texparser.LatexParserResults;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class CitationFinder {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(CitationFinder.class);
-    private static final String TEX_EXT = ".tex";
-    private final Path directory;
-
-    private LatexParserResults latexParserResults;
-
-    public CitationFinder(Path directory) {
-        this.directory = directory;
-    }
-
-    public Collection<Citation> searchAndParse(String citeKey) throws IOException {
-        if (latexParserResults == null) {
-            if (!Files.exists(directory)) {
-                throw new IOException("Current search directory does not exist: %s".formatted(directory));
-            }
-
-            List<Path> texFiles = searchDirectory(directory);
-            LOGGER.debug("Found tex files: {}", texFiles);
-            latexParserResults = new DefaultLatexParser().parse(texFiles);
-        }
-
-        return latexParserResults.getCitationsByKey(citeKey);
-    }
-
-    /**
-     * @param directory the directory to search for. It is recursively searched.
-     */
-    private List<Path> searchDirectory(Path directory) {
-        LOGGER.debug("Searching directory {}", directory);
-        try (Stream<Path> paths = Files.walk(directory)) {
-            return paths.filter(Files::isRegularFile)
-                        .filter(path -> path.toString().endsWith(TEX_EXT))
-                        .toList();
-        } catch (IOException e) {
-            LOGGER.error("Error while searching files", e);
-            return List.of();
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/logic/texparser/DefaultLatexParser.java b/src/main/java/org/jabref/logic/texparser/DefaultLatexParser.java
index 385c3b8b94e..1e24671c21e 100644
--- a/src/main/java/org/jabref/logic/texparser/DefaultLatexParser.java
+++ b/src/main/java/org/jabref/logic/texparser/DefaultLatexParser.java
@@ -12,7 +12,6 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Optional;
-import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -50,12 +49,6 @@ public class DefaultLatexParser implements LatexParser {
     private static final Pattern INCLUDE_PATTERN = Pattern.compile(
             "\\\\(?:include|input)\\{(?<%s>[^\\}]*)\\}".formatted(INCLUDE_GROUP));
 
-    private final LatexParserResults latexParserResults;
-
-    public DefaultLatexParser() {
-        this.latexParserResults = new LatexParserResults();
-    }
-
     @Override
     public LatexParserResult parse(String citeString) {
         Path path = Path.of("");
@@ -70,6 +63,7 @@ public Optional<LatexParserResult> parse(Path latexFile) {
             LOGGER.error("File does not exist: {}", latexFile);
             return Optional.empty();
         }
+
         LatexParserResult latexParserResult = new LatexParserResult(latexFile);
 
         try (InputStream inputStream = Files.newInputStream(latexFile);
@@ -99,20 +93,9 @@ public Optional<LatexParserResult> parse(Path latexFile) {
 
     @Override
     public LatexParserResults parse(List<Path> latexFiles) {
-        for (Path latexFile : latexFiles) {
-            if (!latexParserResults.isParsed(latexFile)) {
-                parse(latexFile).ifPresent(parsedTex -> latexParserResults.add(latexFile, parsedTex));
-            }
-        }
-
-        Set<Path> nonParsedNestedFiles = latexParserResults.getNonParsedNestedFiles();
-        // Parse all "non-parsed" files referenced by TEX files, recursively.
-        if (!nonParsedNestedFiles.isEmpty()) {
-            // modifies class variable latexParserResults
-            parse(nonParsedNestedFiles.stream().toList());
-        }
-
-        return latexParserResults;
+        LatexParserResults results = new LatexParserResults();
+        latexFiles.forEach(file -> parse(file).ifPresent(result -> results.add(file, result)));
+        return results;
     }
 
     /**
diff --git a/src/main/java/org/jabref/model/texparser/LatexParserResults.java b/src/main/java/org/jabref/model/texparser/LatexParserResults.java
index 63245fea4ea..d09df07408a 100644
--- a/src/main/java/org/jabref/model/texparser/LatexParserResults.java
+++ b/src/main/java/org/jabref/model/texparser/LatexParserResults.java
@@ -28,31 +28,20 @@ public LatexParserResults(LatexParserResult... parsedFiles) {
         }
     }
 
-    public boolean isParsed(Path texFile) {
-        return parsedTexFiles.containsKey(texFile);
-    }
-
     public void add(Path texFile, LatexParserResult parsedFile) {
         parsedTexFiles.put(texFile, parsedFile);
     }
 
+    public LatexParserResult remove(Path texFile) {
+        return parsedTexFiles.remove(texFile);
+    }
+
     public Set<Path> getBibFiles() {
         Set<Path> bibFiles = new HashSet<>();
         parsedTexFiles.values().forEach(result -> bibFiles.addAll(result.getBibFiles()));
         return bibFiles;
     }
 
-    public Set<Path> getNonParsedNestedFiles() {
-        Set<Path> nonParsedNestedFiles = new HashSet<>();
-        for (LatexParserResult result : parsedTexFiles.values()) {
-            nonParsedNestedFiles.addAll(result.getNestedFiles()
-                                            .stream()
-                                            .filter(nestedFile -> !parsedTexFiles.containsKey(nestedFile))
-                                            .toList());
-        }
-        return nonParsedNestedFiles;
-    }
-
     public Multimap<String, Citation> getCitations() {
         Multimap<String, Citation> citations = HashMultimap.create();
         parsedTexFiles.forEach((path, result) -> citations.putAll(result.getCitations()));
@@ -65,6 +54,10 @@ public Collection<Citation> getCitationsByKey(String key) {
         return citations;
     }
 
+    public void clear() {
+        parsedTexFiles.clear();
+    }
+
     @Override
     public boolean equals(Object obj) {
         if (this == obj) {
diff --git a/src/main/java/org/jabref/model/util/DirectoryMonitor.java b/src/main/java/org/jabref/model/util/DirectoryMonitor.java
new file mode 100644
index 00000000000..0678704c8a1
--- /dev/null
+++ b/src/main/java/org/jabref/model/util/DirectoryMonitor.java
@@ -0,0 +1,25 @@
+package org.jabref.model.util;
+
+import org.apache.commons.io.monitor.FileAlterationListener;
+import org.apache.commons.io.monitor.FileAlterationObserver;
+
+public interface DirectoryMonitor {
+    /**
+     * Add an observer to the monitor.
+     *
+     * @param observer The directory to observe.
+     * @param listener The listener to invoke when the directory changes.
+     */
+    void addObserver(FileAlterationObserver observer, FileAlterationListener listener);
+
+    /**
+     * Remove an observer from the monitor.
+     *
+     * @param observer The directory to stop monitoring.
+     */
+    void removeObserver(FileAlterationObserver observer);
+
+    void start();
+
+    void shutdown();
+}
diff --git a/src/main/java/org/jabref/model/util/DirectoryMonitorManager.java b/src/main/java/org/jabref/model/util/DirectoryMonitorManager.java
new file mode 100644
index 00000000000..ba3c6546a8f
--- /dev/null
+++ b/src/main/java/org/jabref/model/util/DirectoryMonitorManager.java
@@ -0,0 +1,36 @@
+package org.jabref.model.util;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.monitor.FileAlterationListener;
+import org.apache.commons.io.monitor.FileAlterationObserver;
+
+public class DirectoryMonitorManager {
+
+    private final DirectoryMonitor directoryMonitor;
+    private final List<FileAlterationObserver> observers = new ArrayList<>();
+
+    public DirectoryMonitorManager(DirectoryMonitor directoryMonitor) {
+        this.directoryMonitor = directoryMonitor;
+    }
+
+    public void addObserver(FileAlterationObserver observer, FileAlterationListener listener) {
+        directoryMonitor.addObserver(observer, listener);
+        observers.add(observer);
+    }
+
+    public void removeObserver(FileAlterationObserver observer) {
+        directoryMonitor.removeObserver(observer);
+        observers.remove(observer);
+    }
+
+    /**
+     *  Unregister all observers associated with this manager from the directory monitor.
+     *  This method should be called when the library is closed to stop watching observers.
+     */
+    public void unregister() {
+        observers.forEach(directoryMonitor::removeObserver);
+        observers.clear();
+    }
+}
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 21233b43e2f..8e7e5c82d98 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2043,10 +2043,10 @@ LaTeX\ Citations=LaTeX Citations
 Search\ citations\ for\ this\ entry\ in\ LaTeX\ files=Search citations for this entry in LaTeX files
 No\ citations\ found=No citations found
 No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=No LaTeX files containing this entry were found.
+Current\ search\ directory\ does\ not\ exist\:\ %0= Current search directory does not exist: %0
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=Selected entry does not have an associated citation key.
 Current\ search\ directory\:=Current search directory:
 Set\ LaTeX\ file\ directory=Set LaTeX file directory
-Refresh=Refresh
 Import\ entries\ from\ LaTeX\ files=Import entries from LaTeX files
 Import\ new\ entries=Import new entries
 Group\ color=Group color

From a3b71c6222a2995418ecbf9baf108f17e02edbba Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 29 Apr 2024 09:30:38 +0200
Subject: [PATCH 11/54] Make newcomer message even more welcoming (#11243)

---
 .github/workflows/add-greeting-to-issue.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/add-greeting-to-issue.yml b/.github/workflows/add-greeting-to-issue.yml
index 497a43d3697..b94650f1a62 100644
--- a/.github/workflows/add-greeting-to-issue.yml
+++ b/.github/workflows/add-greeting-to-issue.yml
@@ -20,6 +20,10 @@ jobs:
       with:
         issue-number: ${{ github.event.issue.number || github.event.pull_request.number }}
         body: |
-            As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.
+          Welcome to the vibrant world of open-source development with JabRef!
 
-            Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's [Gitter](https://gitter.im/JabRef/jabref) chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.
+          Newcomers, we're excited to have you on board. Start by exploring our [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) guidelines, and don't forget to check out our [workspace setup guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) to get started smoothly.
+
+          Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref). And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.
+
+          Happy coding! 🚀

From 3de7e146f0d57c2a3d8f71d723429e27f6b3cfa9 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 29 Apr 2024 11:33:10 +0200
Subject: [PATCH 12/54] Fix artifact creation for forks (#11247)

---
 .github/workflows/deployment-jdk-ea.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
index eadf8903387..340a566df64 100644
--- a/.github/workflows/deployment-jdk-ea.yml
+++ b/.github/workflows/deployment-jdk-ea.yml
@@ -214,21 +214,19 @@ jobs:
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image and installer
-        if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage jlinkZip
       - name: Package application image
-        if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Rename files
-        if: (matrix.os != 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os != 'macos-latest')
         shell: pwsh
         run: |
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Repack deb file for Debian
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-latest')
         shell: bash
         run: |
           cd build/distribution
@@ -239,7 +237,6 @@ jobs:
           rm debian-binary control.tar.* data.tar.*
           mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
       - name: Rename files with JDK version
-        if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           for file in build/distribution/*.*; do

From 529c201d27b3a74a3b0a85169f51e68208b7b244 Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Mon, 29 Apr 2024 12:38:11 +0300
Subject: [PATCH 13/54] Hide the side pane after closing all panels within it
 (#11241)

* Add InvalidationListener to sidePane

* Fix missing width listener

---------

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
---
 src/main/java/org/jabref/gui/frame/JabRefFrame.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/frame/JabRefFrame.java b/src/main/java/org/jabref/gui/frame/JabRefFrame.java
index 84a34f53966..e154ae6f7e6 100644
--- a/src/main/java/org/jabref/gui/frame/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/frame/JabRefFrame.java
@@ -9,6 +9,7 @@
 import java.util.function.Supplier;
 
 import javafx.application.Platform;
+import javafx.beans.InvalidationListener;
 import javafx.beans.binding.Bindings;
 import javafx.beans.binding.StringBinding;
 import javafx.collections.transformation.FilteredList;
@@ -212,7 +213,9 @@ private void initLayout() {
 
         splitPane.getItems().addAll(tabbedPane);
         SplitPane.setResizableWithParent(sidePane, false);
-        EasyBind.subscribe(sidePane.widthProperty(), c -> updateSidePane());
+        sidePane.widthProperty().addListener(c -> updateSidePane());
+        sidePane.getChildren().addListener((InvalidationListener) c -> updateSidePane());
+        updateSidePane();
         setCenter(splitPane);
     }
 

From 9f2418bbed23802a4c828a934d8cbef5bf5204b4 Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Mon, 29 Apr 2024 11:41:48 +0200
Subject: [PATCH 14/54] Remove download when html file (#11227)

* Remove download when html file

Fixes #10149

* changelog

* remove test

* Fix behavior when file is duplicate file

* Refine comments

* Keep html file when downloading inside the entry editor

* Add some dots

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
---
 CHANGELOG.md                                  |  7 +-
 .../jabref/gui/entryeditor/EntryEditor.java   |  2 +
 .../externalfiles/DownloadFullTextAction.java |  3 +-
 .../gui/externalfiles/ImportHandler.java      |  6 +-
 .../gui/fieldeditors/LinkedFileViewModel.java | 16 ++--
 .../gui/fieldeditors/LinkedFilesEditor.java   |  2 +-
 .../LinkedFilesEditorViewModel.java           |  2 +-
 .../linkedfile/AttachFileFromURLAction.java   |  2 +-
 .../linkedfile/DownloadLinkedFileAction.java  | 83 ++++++++++++-------
 .../RedownloadMissingFilesAction.java         |  5 +-
 .../logic/util/io/FileNameUniqueness.java     | 13 ++-
 .../java/org/jabref/model/entry/BibEntry.java |  6 +-
 src/main/resources/l10n/JabRef_en.properties  |  4 +-
 .../fieldeditors/LinkedFileViewModelTest.java | 58 +++++--------
 .../DownloadLinkedFileActionTest.java         | 67 ++++++++++++++-
 15 files changed, 177 insertions(+), 99 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 134ec7736be..a2ffda77a00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,14 +23,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Changed
 
 - We replaced the word "Key bindings" with "Keyboard shortcuts" in the Preferences tab. [#11153](https://github.com/JabRef/jabref/pull/11153)
-- We slightly improved the duplicate check if ISBN numbers are present. [#8885](https://github.com/JabRef/jabref/issues/8885)
+- We slightly improved the duplicate check if ISBNs are present. [#8885](https://github.com/JabRef/jabref/issues/8885)
+- JabRef no longer downloads HTML files of websites when a PDF was not found. [#10149](https://github.com/JabRef/jabref/issues/10149)
 
 ### Fixed
 
-- We fixed an issue where entry type with duplicate fields prevented opening existing libraries with custom entry types [#11127](https://github.com/JabRef/jabref/issues/11127)
+- We fixed an issue where entry type with duplicate fields prevented opening existing libraries with custom entry types. [#11127](https://github.com/JabRef/jabref/issues/11127)
 - We fixed an issue where Markdown rendering removed braces from the text. [#10928](https://github.com/JabRef/jabref/issues/10928)
 - We fixed an issue when the file was flagged as changed on disk in the case of content selectors or groups. [#9064](https://github.com/JabRef/jabref/issues/9064)
-- We fixed crash on opening the entry editor when auto completion is enabled. [#11188](https://github.com/JabRef/jabref/issues/11188)
+- We fixed crash on opening the entry editor when auto-completion is enabled. [#11188](https://github.com/JabRef/jabref/issues/11188)
 - We fixed the usage of the key binding for "Clear search" (default: <kbd>Escape</kbd>). [#10764](https://github.com/JabRef/jabref/issues/10764)
 - We fixed an issue where library shown as unsaved and marked (*) after accepting changes made externally to the file. [#11027](https://github.com/JabRef/jabref/issues/11027)
 
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index 220d11e2299..759c46fc0ad 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -74,6 +74,8 @@
  * <p>
  * EntryEditor also registers itself to the event bus, receiving events whenever a field of the entry changes, enabling
  * the text fields to update themselves if the change is made from somewhere else.
+ * <p>
+ * The editors for fields are created via {@link org.jabref.gui.fieldeditors.FieldEditors}.
  */
 public class EntryEditor extends BorderPane {
 
diff --git a/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java
index 321f31bc31f..7197f9c2422 100644
--- a/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java
+++ b/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java
@@ -141,8 +141,7 @@ private void addLinkedFileFromURL(BibDatabaseContext databaseContext, URL url, B
                     taskExecutor,
                     dialogService,
                     preferences);
-
-            onlineFile.download();
+            onlineFile.download(true);
         } else {
             dialogService.notify(Localization.lang("Full text document for entry %0 already linked.",
                     entry.getCitationKey().orElse(Localization.lang("undefined"))));
diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
index de4ac03f686..8465c4305f6 100644
--- a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -276,7 +276,7 @@ public void downloadLinkedFiles(BibEntry entry) {
                                  taskExecutor,
                                  dialogService,
                                  preferencesService
-                         ).download()
+                         ).download(false)
                  );
         }
     }
@@ -405,13 +405,13 @@ public void importEntriesWithDuplicateCheck(BibDatabaseContext database, List<Bi
         boolean firstEntry = true;
         for (BibEntry entry : entriesToAdd) {
             if (firstEntry) {
-                LOGGER.debug("First entry to import, we use BREAK");
+                LOGGER.debug("First entry to import, we use BREAK (\"Ask every time\") as decision");
                 importEntryWithDuplicateCheck(database, entry, BREAK);
                 firstEntry = false;
                 continue;
             }
             if (preferencesService.getMergeDialogPreferences().shouldMergeApplyToAllEntries()) {
-                var decision = preferencesService.getMergeDialogPreferences().getAllEntriesDuplicateResolverDecision();
+                DuplicateResolverDialog.DuplicateResolverResult decision = preferencesService.getMergeDialogPreferences().getAllEntriesDuplicateResolverDecision();
                 LOGGER.debug("Not first entry, pref flag is true, we use {}", decision);
                 importEntryWithDuplicateCheck(database, entry, decision);
             } else {
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index a1b223e40f7..8ae9f3f0ba2 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -384,8 +384,11 @@ public void edit() {
         });
     }
 
+    /**
+     * @implNote Similar method {@link org.jabref.gui.linkedfile.RedownloadMissingFilesAction#redownloadMissing}
+     */
     public void redownload() {
-        LOGGER.info("Redownloading file from " + linkedFile.getSourceUrl());
+        LOGGER.info("Redownloading file from {}", linkedFile.getSourceUrl());
         if (linkedFile.getSourceUrl().isEmpty() || !LinkedFile.isOnlineLink(linkedFile.getSourceUrl())) {
             throw new UnsupportedOperationException("In order to download the file, the source url has to be an online link");
         }
@@ -400,13 +403,14 @@ public void redownload() {
                 dialogService,
                 preferencesService.getFilePreferences(),
                 taskExecutor,
-                fileName);
+                fileName,
+                true);
         downloadProgress.bind(downloadLinkedFileAction.downloadProgress());
         downloadLinkedFileAction.execute();
     }
 
-    public void download() {
-        LOGGER.info("Downloading file from " + linkedFile.getSourceUrl());
+    public void download(boolean keepHtmlLink) {
+        LOGGER.info("Downloading file from {}", linkedFile.getSourceUrl());
         if (!linkedFile.isOnlineLink()) {
             throw new UnsupportedOperationException("In order to download the file it has to be an online link");
         }
@@ -418,7 +422,9 @@ public void download() {
                 linkedFile.getLink(),
                 dialogService,
                 preferencesService.getFilePreferences(),
-                taskExecutor);
+                taskExecutor,
+                "",
+                keepHtmlLink);
         downloadProgress.bind(downloadLinkedFileAction.downloadProgress());
         downloadLinkedFileAction.execute();
     }
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
index b871e61ef91..a0ec54d323f 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
@@ -376,7 +376,7 @@ public void execute() {
                 case EDIT_FILE_LINK -> linkedFile.edit();
                 case OPEN_FILE -> linkedFile.open();
                 case OPEN_FOLDER -> linkedFile.openFolder();
-                case DOWNLOAD_FILE -> linkedFile.download();
+                case DOWNLOAD_FILE -> linkedFile.download(true);
                 case REDOWNLOAD_FILE -> linkedFile.redownload();
                 case RENAME_FILE_TO_PATTERN -> linkedFile.renameToSuggestion();
                 case RENAME_FILE_TO_NAME -> linkedFile.askForNameAndRename();
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
index 91d0dbf6690..005ef6e75ff 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
@@ -279,7 +279,7 @@ private void addFromURLAndDownload(URL url) {
                 dialogService,
                 preferences);
         files.add(onlineFile);
-        onlineFile.download();
+        onlineFile.download(true);
     }
 
     public void deleteFile(LinkedFileViewModel file) {
diff --git a/src/main/java/org/jabref/gui/linkedfile/AttachFileFromURLAction.java b/src/main/java/org/jabref/gui/linkedfile/AttachFileFromURLAction.java
index 08c9240b0a2..e95af5e25a6 100644
--- a/src/main/java/org/jabref/gui/linkedfile/AttachFileFromURLAction.java
+++ b/src/main/java/org/jabref/gui/linkedfile/AttachFileFromURLAction.java
@@ -68,7 +68,7 @@ public void execute() {
                              taskExecutor,
                              dialogService,
                              preferencesService);
-            onlineFile.download();
+            onlineFile.download(true);
         } catch (MalformedURLException exception) {
             dialogService.showErrorDialogAndWait(Localization.lang("Invalid URL"), exception);
         }
diff --git a/src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java b/src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java
index 53684fe43f7..6df76576628 100644
--- a/src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java
+++ b/src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java
@@ -6,6 +6,8 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 
 import javax.net.ssl.HostnameVerifier;
@@ -55,6 +57,7 @@ public class DownloadLinkedFileAction extends SimpleCommand {
     private final String downloadUrl;
     private final FilePreferences filePreferences;
     private final TaskExecutor taskExecutor;
+    private final boolean keepHtmlLink;
 
     private final BibDatabaseContext databaseContext;
 
@@ -68,7 +71,8 @@ public DownloadLinkedFileAction(BibDatabaseContext databaseContext,
                                     DialogService dialogService,
                                     FilePreferences filePreferences,
                                     TaskExecutor taskExecutor,
-                                    String suggestedName) {
+                                    String suggestedName,
+                                    boolean keepHtmlLink) {
         this.databaseContext = databaseContext;
         this.entry = entry;
         this.linkedFile = linkedFile;
@@ -77,10 +81,14 @@ public DownloadLinkedFileAction(BibDatabaseContext databaseContext,
         this.dialogService = dialogService;
         this.filePreferences = filePreferences;
         this.taskExecutor = taskExecutor;
+        this.keepHtmlLink = keepHtmlLink;
 
         this.linkedFileHandler = new LinkedFileHandler(linkedFile, entry, databaseContext, filePreferences);
     }
 
+    /**
+     * Downloads the given linked file to the first existing file directory. It keeps HTML files as URLs.
+     */
     public DownloadLinkedFileAction(BibDatabaseContext databaseContext,
                                     BibEntry entry,
                                     LinkedFile linkedFile,
@@ -88,12 +96,12 @@ public DownloadLinkedFileAction(BibDatabaseContext databaseContext,
                                     DialogService dialogService,
                                     FilePreferences filePreferences,
                                     TaskExecutor taskExecutor) {
-        this(databaseContext, entry, linkedFile, downloadUrl, dialogService, filePreferences, taskExecutor, "");
+        this(databaseContext, entry, linkedFile, downloadUrl, dialogService, filePreferences, taskExecutor, "", true);
     }
 
     @Override
     public void execute() {
-        LOGGER.info("Downloading file from " + downloadUrl);
+        LOGGER.info("Downloading file from {}", downloadUrl);
         if (downloadUrl.isEmpty() || !LinkedFile.isOnlineLink(downloadUrl)) {
             throw new UnsupportedOperationException("In order to download the file, the url has to be an online link");
         }
@@ -132,51 +140,64 @@ private void doDownload(Path targetDirectory, URLDownload urlDownload) {
         taskExecutor.execute(downloadTask);
     }
 
-    private void onSuccess(Path targetDirectory, Path destination) {
+    /**
+     * @param targetDirectory The directory to store the file into. Is an absolute path.
+     */
+    private void onSuccess(Path targetDirectory, Path downloadedFile) {
+        assert targetDirectory.isAbsolute();
+
         boolean isDuplicate;
         boolean isHtml;
         try {
-            isDuplicate = FileNameUniqueness.isDuplicatedFile(targetDirectory, destination.getFileName(), dialogService);
+            isDuplicate = FileNameUniqueness.isDuplicatedFile(targetDirectory, downloadedFile.getFileName(), dialogService);
         } catch (IOException e) {
             LOGGER.error("FileNameUniqueness.isDuplicatedFile failed", e);
             return;
         }
 
         if (isDuplicate) {
-            destination = targetDirectory.resolve(
-                    FileNameUniqueness.eraseDuplicateMarks(destination.getFileName()));
-
-            linkedFile.setLink(FileUtil.relativize(destination,
-                    databaseContext.getFileDirectories(filePreferences)).toString());
+            // We do not add duplicate files.
+            // The downloaded file was deleted in {@link org.jabref.logic.util.io.FileNameUniqueness.isDuplicatedFile]}
+            LOGGER.info("File {} already exists in target directory {}.", downloadedFile.getFileName(), targetDirectory);
+            return;
+        }
 
-            isHtml = linkedFile.getFileType().equals(StandardExternalFileType.URL.getName());
+        // we need to call LinkedFileViewModel#fromFile, because we need to make the path relative to the configured directories
+        LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(
+                downloadedFile,
+                databaseContext.getFileDirectories(filePreferences),
+                filePreferences);
+        if (newLinkedFile.getDescription().isEmpty() && !linkedFile.getDescription().isEmpty()) {
+            newLinkedFile.setDescription((linkedFile.getDescription()));
+        }
+        if (linkedFile.getSourceUrl().isEmpty() && LinkedFile.isOnlineLink(linkedFile.getLink())) {
+            newLinkedFile.setSourceURL(linkedFile.getLink());
         } else {
-            // we need to call LinkedFileViewModel#fromFile, because we need to make the path relative to the configured directories
-            LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(
-                    destination,
-                    databaseContext.getFileDirectories(filePreferences),
-                    filePreferences);
-            if (newLinkedFile.getDescription().isEmpty() && !linkedFile.getDescription().isEmpty()) {
-                newLinkedFile.setDescription((linkedFile.getDescription()));
-            }
-            if (linkedFile.getSourceUrl().isEmpty() && LinkedFile.isOnlineLink(linkedFile.getLink())) {
-                newLinkedFile.setSourceURL(linkedFile.getLink());
-            } else {
-                newLinkedFile.setSourceURL(linkedFile.getSourceUrl());
-            }
-            entry.replaceDownloadedFile(linkedFile.getLink(), newLinkedFile);
-            isHtml = newLinkedFile.getFileType().equals(StandardExternalFileType.URL.getName());
+            newLinkedFile.setSourceURL(linkedFile.getSourceUrl());
         }
 
-        // Notify in bar when the file type is HTML.
+        isHtml = newLinkedFile.getFileType().equals(StandardExternalFileType.URL.getName());
         if (isHtml) {
-            dialogService.notify(Localization.lang("Downloaded website as an HTML file."));
-            LOGGER.debug("Downloaded website {} as an HTML file at {}", linkedFile.getLink(), destination);
+            if (this.keepHtmlLink) {
+                dialogService.notify(Localization.lang("Download '%0' was a HTML file. Keeping URL.", downloadUrl));
+            } else {
+                dialogService.notify(Localization.lang("Download '%0' was a HTML file. Removed.", downloadUrl));
+                List<LinkedFile> newFiles = new ArrayList<>(entry.getFiles());
+                newFiles.remove(linkedFile);
+                entry.setFiles(newFiles);
+                try {
+                    Files.delete(downloadedFile);
+                } catch (IOException e) {
+                    LOGGER.error("Could not delete downloaded file {}.", downloadedFile, e);
+                }
+            }
+        } else {
+            entry.replaceDownloadedFile(linkedFile.getLink(), newLinkedFile);
         }
     }
 
     private void onFailure(URLDownload urlDownload, Exception ex) {
-        LOGGER.error("Error downloading from URL: " + urlDownload, ex);
+        LOGGER.error("Error downloading from URL: {}", urlDownload, ex);
         String fetcherExceptionMessage = ex.getMessage();
         String failedTitle = Localization.lang("Failed to download from URL");
         int statusCode;
@@ -261,7 +282,7 @@ private Optional<ExternalFileType> inferFileTypeFromMimeType(URLDownload urlDown
         String mimeType = urlDownload.getMimeType();
 
         if (mimeType != null) {
-            LOGGER.debug("MIME Type suggested: " + mimeType);
+            LOGGER.debug("MIME Type suggested: {}", mimeType);
             return ExternalFileTypes.getExternalFileTypeByMimeType(mimeType, filePreferences);
         } else {
             return Optional.empty();
diff --git a/src/main/java/org/jabref/gui/linkedfile/RedownloadMissingFilesAction.java b/src/main/java/org/jabref/gui/linkedfile/RedownloadMissingFilesAction.java
index f08933976cb..3a69061b10f 100644
--- a/src/main/java/org/jabref/gui/linkedfile/RedownloadMissingFilesAction.java
+++ b/src/main/java/org/jabref/gui/linkedfile/RedownloadMissingFilesAction.java
@@ -56,6 +56,9 @@ public void execute() {
         }
     }
 
+    /**
+     * @implNote Similar method {@link org.jabref.gui.fieldeditors.LinkedFileViewModel#redownload}
+     */
     private void redownloadMissing(BibDatabaseContext databaseContext) {
         LOGGER.info("Redownloading missing files");
         databaseContext.getEntries().forEach(entry -> {
@@ -71,7 +74,7 @@ private void redownloadMissing(BibDatabaseContext databaseContext) {
                 String fileName = Path.of(linkedFile.getLink()).getFileName().toString();
 
                 DownloadLinkedFileAction downloadAction = new DownloadLinkedFileAction(this.databaseContext, entry,
-                        linkedFile, linkedFile.getSourceUrl(), dialogService, filePreferences, taskExecutor, fileName);
+                        linkedFile, linkedFile.getSourceUrl(), dialogService, filePreferences, taskExecutor, fileName, true);
                 downloadAction.execute();
             });
         });
diff --git a/src/main/java/org/jabref/logic/util/io/FileNameUniqueness.java b/src/main/java/org/jabref/logic/util/io/FileNameUniqueness.java
index 2c1456d13cd..44a73e0ae71 100644
--- a/src/main/java/org/jabref/logic/util/io/FileNameUniqueness.java
+++ b/src/main/java/org/jabref/logic/util/io/FileNameUniqueness.java
@@ -11,7 +11,12 @@
 import org.jabref.gui.DialogService;
 import org.jabref.logic.l10n.Localization;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public class FileNameUniqueness {
+    private static final Logger LOGGER = LoggerFactory.getLogger(FileNameUniqueness.class);
+
     private static final Pattern DUPLICATE_MARK_PATTERN = Pattern.compile("(.*) \\(\\d+\\)");
 
     /**
@@ -61,7 +66,6 @@ public static String getNonOverWritingFileName(Path targetDirectory, String file
      * @throws IOException Fail when the file is not exist or something wrong when reading the file
      */
     public static boolean isDuplicatedFile(Path directory, Path fileName, DialogService dialogService) throws IOException {
-
         Objects.requireNonNull(directory);
         Objects.requireNonNull(fileName);
         Objects.requireNonNull(dialogService);
@@ -83,10 +87,11 @@ public static boolean isDuplicatedFile(Path directory, Path fileName, DialogServ
 
         while (Files.exists(originalFile)) {
             if (com.google.common.io.Files.equal(originalFile.toFile(), duplicateFile.toFile())) {
-                if (duplicateFile.toFile().delete()) {
+                try {
+                    Files.delete(duplicateFile);
                     dialogService.notify(Localization.lang("File '%1' is a duplicate of '%0'. Keeping '%0'", originalFileName, fileName));
-                } else {
-                    dialogService.notify(Localization.lang("File '%1' is a duplicate of '%0'. Keeping both due to deletion error", originalFileName, fileName));
+                } catch (IOException e) {
+                    LOGGER.error("File '{}' is a duplicate of '{}'. Could not delete '{}'.", fileName, originalFileName, fileName);
                 }
                 return true;
             }
diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
index 19b33f257fb..6f463422a36 100644
--- a/src/main/java/org/jabref/model/entry/BibEntry.java
+++ b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -613,11 +613,11 @@ public Optional<FieldChange> setField(Field field, String value, EntriesEventSou
         }
 
         String oldValue = getField(field).orElse(null);
-        boolean isNewField = oldValue == null;
         if (value.equals(oldValue)) {
             return Optional.empty();
         }
 
+        boolean isNewField = oldValue == null;
         changed = true;
 
         invalidateFieldCache(field);
@@ -1062,15 +1062,15 @@ public BibEntry withFiles(List<LinkedFile> files) {
      * Gets a list of linked files.
      *
      * @return the list of linked files, is never null but can be empty.
-     * Changes to the underlying list will have no effect on the entry itself. Use {@link #addFile(LinkedFile)}
+     * Changes to the underlying list will have no effect on the entry itself. Use {@link #addFile(LinkedFile)}.
      */
     public List<LinkedFile> getFiles() {
-        // Extract the path
         Optional<String> oldValue = getField(StandardField.FILE);
         if (oldValue.isEmpty()) {
             return new ArrayList<>(); // Return new ArrayList because emptyList is immutable
         }
 
+        // Extract the path
         return FileFieldParser.parse(oldValue.get());
     }
 
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 8e7e5c82d98..fdb5076f8c5 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -276,7 +276,8 @@ Donate\ to\ JabRef=Donate to JabRef
 
 Download\ file=Download file
 
-Downloaded\ website\ as\ an\ HTML\ file.=Downloaded website as an HTML file.
+Download\ '%0'\ was\ a\ HTML\ file.\ Removed.=Download '%0' was a HTML file. Removed.
+Download\ '%0'\ was\ a\ HTML\ file.\ Keeping\ URL.=Download '%0' was a HTML file. Keeping URL.
 
 duplicate\ removal=duplicate removal
 
@@ -2402,7 +2403,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Convert timestamp field
 New\ entry\ by\ type=New entry by type
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=File '%1' is a duplicate of '%0'. Keeping '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=File '%1' is a duplicate of '%0'. Keeping both due to deletion error
 
 Enable\ field\ formatters=Enable field formatters
 Entry\ Type=Entry Type
diff --git a/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java b/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
index 78b765ec3f6..18efb37fd94 100644
--- a/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
+++ b/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
@@ -29,7 +29,6 @@
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.PreferencesService;
-import org.jabref.testutils.category.FetcherTest;
 import org.jabref.testutils.category.GUITest;
 
 import org.junit.jupiter.api.AfterEach;
@@ -37,6 +36,9 @@
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.api.io.TempDir;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.testfx.framework.junit5.ApplicationExtension;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -181,8 +183,12 @@ void deleteWhenDialogCancelledReturnsFalseAndDoesNotRemoveFile() {
         assertTrue(Files.exists(tempFile));
     }
 
-    @Test
-    void downloadHtmlFileCausesWarningDisplay() throws MalformedURLException {
+    @ParameterizedTest
+    @CsvSource({
+            "true, Download 'https://www.google.com/' was a HTML file. Keeping URL.",
+            "false, Download 'https://www.google.com/' was a HTML file. Removed."
+    })
+    void downloadHtmlFileCausesWarningDisplay(Boolean keepHtmlLink, String warningText) throws MalformedURLException {
         when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(true);
         when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
         when(filePreferences.getFileDirectoryPattern()).thenReturn("[entrytype]");
@@ -194,39 +200,9 @@ void downloadHtmlFileCausesWarningDisplay() throws MalformedURLException {
 
         LinkedFileViewModel viewModel = new LinkedFileViewModel(linkedFile, entry, databaseContext, new CurrentThreadTaskExecutor(), dialogService, preferences);
 
-        viewModel.download();
+        viewModel.download(keepHtmlLink);
 
-        verify(dialogService, atLeastOnce()).notify("Downloaded website as an HTML file.");
-    }
-
-    @FetcherTest
-    @Test
-    void downloadHtmlWhenLinkedFilePointsToHtml() throws MalformedURLException {
-        // use google as test url, wiley is protected by CloudFlare
-        String url = "https://google.com";
-        String fileType = StandardExternalFileType.URL.getName();
-        linkedFile = new LinkedFile(new URL(url), fileType);
-
-        when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(true);
-        when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
-        when(filePreferences.getFileDirectoryPattern()).thenReturn("[entrytype]");
-
-        databaseContext.setDatabasePath(tempFile);
-
-        LinkedFileViewModel viewModel = new LinkedFileViewModel(linkedFile, entry, databaseContext, new CurrentThreadTaskExecutor(), dialogService, preferences);
-
-        viewModel.download();
-
-        List<LinkedFile> linkedFiles = entry.getFiles();
-
-        for (LinkedFile file: linkedFiles) {
-            if ("Misc/asdf.html".equalsIgnoreCase(file.getLink())) {
-                assertEquals("URL", file.getFileType());
-                return;
-            }
-        }
-        // If the file was not found among the linked files to the entry
-        fail();
+        verify(dialogService, atLeastOnce()).notify(warningText);
     }
 
     @Test
@@ -290,9 +266,11 @@ void mimeTypeStringWithParameterIsReturnedAsWithoutParameter() {
         assertEquals("URL", actual);
     }
 
-    @Test
-    @FetcherTest
-    void downloadPdfFileWhenLinkedFilePointsToPdfUrl() throws MalformedURLException {
+    // We cannot use "@FetcherTest" annotation, because a @FetcherTest does not fire up a GUI environment (which is needed for this test)
+    // @FetcherTest
+    @ParameterizedTest
+    @ValueSource(booleans = {true, false})
+    void downloadPdfFileWhenLinkedFilePointsToPdfUrl(boolean keepHtml) throws MalformedURLException {
         linkedFile = new LinkedFile(new URL("http://arxiv.org/pdf/1207.0408v1"), "pdf");
         // Needed Mockito stubbing methods to run test
         when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(true);
@@ -302,7 +280,9 @@ void downloadPdfFileWhenLinkedFilePointsToPdfUrl() throws MalformedURLException
         databaseContext.setDatabasePath(tempFile);
 
         LinkedFileViewModel viewModel = new LinkedFileViewModel(linkedFile, entry, databaseContext, new CurrentThreadTaskExecutor(), dialogService, preferences);
-        viewModel.download();
+
+        // TODO: Rewrite using WireMock
+        viewModel.download(keepHtml);
 
         // Loop through downloaded files to check for filetype='pdf'
         List<LinkedFile> linkedFiles = entry.getFiles();
diff --git a/src/test/java/org/jabref/gui/linkedfile/DownloadLinkedFileActionTest.java b/src/test/java/org/jabref/gui/linkedfile/DownloadLinkedFileActionTest.java
index 80791f86bba..067b21f0cc2 100644
--- a/src/test/java/org/jabref/gui/linkedfile/DownloadLinkedFileActionTest.java
+++ b/src/test/java/org/jabref/gui/linkedfile/DownloadLinkedFileActionTest.java
@@ -26,6 +26,8 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.ArgumentMatchers.any;
@@ -33,6 +35,11 @@
 import static org.mockito.Mockito.when;
 
 class DownloadLinkedFileActionTest {
+
+    // Required for keepsHtmlEntry
+    @TempDir
+    Path tempFolder;
+
     private BibEntry entry;
 
     private final BibDatabaseContext databaseContext = mock(BibDatabaseContext.class);
@@ -84,8 +91,9 @@ void replacesLinkedFiles(@TempDir Path tempFolder) throws Exception {
         assertEquals(List.of(new LinkedFile("", tempFolder.resolve("asdf.pdf"), "PDF", url)), entry.getFiles());
     }
 
-    @Test
-    void doesntReplaceSourceURL(@TempDir Path tempFolder) throws Exception {
+    @ParameterizedTest
+    @ValueSource(booleans = {true, false})
+    void doesntReplaceSourceURL(boolean keepHtml) throws Exception {
         String url = "http://arxiv.org/pdf/1207.0408v1";
 
         LinkedFile linkedFile = new LinkedFile(new URL(url), "");
@@ -120,9 +128,62 @@ void doesntReplaceSourceURL(@TempDir Path tempFolder) throws Exception {
                 dialogService,
                 preferences.getFilePreferences(),
                 new CurrentThreadTaskExecutor(),
-                Path.of(linkedFile.getLink()).getFileName().toString());
+                Path.of(linkedFile.getLink()).getFileName().toString(),
+                keepHtml);
         downloadLinkedFileAction2.execute();
 
         assertEquals(List.of(new LinkedFile("", tempFolder.resolve("asdf.pdf"), "PDF", url)), entry.getFiles());
     }
+
+    @Test
+    void keepsHtmlEntry(@TempDir Path tempFolder) throws Exception {
+        String url = "https://blog.fefe.de/?ts=98e04151";
+
+        LinkedFile linkedFile = new LinkedFile(new URL(url), "");
+        when(databaseContext.getFirstExistingFileDir(any())).thenReturn(Optional.of(tempFolder));
+        when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
+        when(filePreferences.getFileDirectoryPattern()).thenReturn("");
+
+        entry.setFiles(List.of(linkedFile));
+
+        BibEntry expected = (BibEntry) entry.clone();
+
+        DownloadLinkedFileAction downloadLinkedFileAction = new DownloadLinkedFileAction(
+                databaseContext,
+                entry,
+                linkedFile,
+                linkedFile.getLink(),
+                dialogService,
+                preferences.getFilePreferences(),
+                new CurrentThreadTaskExecutor());
+        downloadLinkedFileAction.execute();
+
+        assertEquals(expected, entry);
+    }
+
+    @Test
+    void removesHtmlEntry(@TempDir Path tempFolder) throws Exception {
+        String url = "https://blog.fefe.de/?ts=98e04151";
+
+        LinkedFile linkedFile = new LinkedFile(new URL(url), "");
+        when(databaseContext.getFirstExistingFileDir(any())).thenReturn(Optional.of(tempFolder));
+        when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
+        when(filePreferences.getFileDirectoryPattern()).thenReturn("");
+
+        entry.setFiles(List.of(linkedFile));
+
+        DownloadLinkedFileAction downloadLinkedFileAction = new DownloadLinkedFileAction(
+                databaseContext,
+                entry,
+                linkedFile,
+                linkedFile.getLink(),
+                dialogService,
+                preferences.getFilePreferences(),
+                new CurrentThreadTaskExecutor(),
+                "",
+                false);
+        downloadLinkedFileAction.execute();
+
+        assertEquals(new BibEntry().withCitationKey("asdf"), entry);
+    }
 }

From 04479ca2fd5c07b724a92ad5bedbb814e42b0108 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 14:37:18 +0000
Subject: [PATCH 15/54] Bump src/main/resources/csl-styles from `af6f50b` to
 `32348cb` (#11258)

Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `af6f50b` to `32348cb`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](https://github.com/citation-style-language/styles/compare/af6f50b080190ccc7ba0c83906fe36c5ece85ce5...32348cb790b809081a0ff42ce81f6bcba050e4de)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-styles
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 src/main/resources/csl-styles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
index af6f50b0801..32348cb790b 160000
--- a/src/main/resources/csl-styles
+++ b/src/main/resources/csl-styles
@@ -1 +1 @@
-Subproject commit af6f50b080190ccc7ba0c83906fe36c5ece85ce5
+Subproject commit 32348cb790b809081a0ff42ce81f6bcba050e4de

From a3e6b19d9419018d5353a8bd0c9c28f0f112ab03 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 14:55:20 +0000
Subject: [PATCH 16/54] Bump com.dlsc.gemsfx:gemsfx from 2.9.0 to 2.10.0
 (#11259)

Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.9.0 to 2.10.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/jreleaser.yml)
- [Commits](https://github.com/dlsc-software-consulting-gmbh/GemsFX/compare/v2.9.0...v2.10.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 28db2f20df6..472fbfdafd5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -218,7 +218,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.9.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.10.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.openjfx'

From adf1e37043b91b000fd2924caafe28a29e341188 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 14:56:15 +0000
Subject: [PATCH 17/54] Bump com.puppycrawl.tools:checkstyle from 10.15.0 to
 10.16.0 (#11260)

Bumps [com.puppycrawl.tools:checkstyle](https://github.com/checkstyle/checkstyle) from 10.15.0 to 10.16.0.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-10.15.0...checkstyle-10.16.0)

---
updated-dependencies:
- dependency-name: com.puppycrawl.tools:checkstyle
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 472fbfdafd5..75acf92e208 100644
--- a/build.gradle
+++ b/build.gradle
@@ -311,7 +311,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.15.0'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.16.0'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

From 0adea6553be66e0d7e31210562e32edc8b6191a5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 14:57:56 +0000
Subject: [PATCH 18/54] Bump org.xmlunit:xmlunit-core from 2.9.1 to 2.10.0
 (#11261)

Bumps [org.xmlunit:xmlunit-core](https://github.com/xmlunit/xmlunit) from 2.9.1 to 2.10.0.
- [Release notes](https://github.com/xmlunit/xmlunit/releases)
- [Changelog](https://github.com/xmlunit/xmlunit/blob/main/RELEASE_NOTES.md)
- [Commits](https://github.com/xmlunit/xmlunit/compare/v2.9.1...v2.10.0)

---
updated-dependencies:
- dependency-name: org.xmlunit:xmlunit-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 75acf92e208..6e9e2de3b67 100644
--- a/build.gradle
+++ b/build.gradle
@@ -303,7 +303,7 @@ dependencies {
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
     testImplementation 'org.mockito:mockito-core:5.11.0'
-    testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
+    testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.3.0'

From 90acb03a6c0533ee04e8f794bc9168848f882e99 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 14:59:45 +0000
Subject: [PATCH 19/54] Bump org.openrewrite.rewrite from 6.11.2 to 6.12.0
 (#11262)

Bumps org.openrewrite.rewrite from 6.11.2 to 6.12.0.

---
updated-dependencies:
- dependency-name: org.openrewrite.rewrite
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 6e9e2de3b67..77dd961a65c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -28,7 +28,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.11.2'
+    id 'org.openrewrite.rewrite' version '6.12.0'
 }
 
 // Enable following for debugging

From 5cff1ad7615728924b6f30ad37e9f9edc7092694 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:06:14 +0000
Subject: [PATCH 20/54] Bump lycheeverse/lychee-action from 1.9.3 to 1.10.0
 (#11264)

Bumps [lycheeverse/lychee-action](https://github.com/lycheeverse/lychee-action) from 1.9.3 to 1.10.0.
- [Release notes](https://github.com/lycheeverse/lychee-action/releases)
- [Commits](https://github.com/lycheeverse/lychee-action/compare/v1.9.3...v1.10.0)

---
updated-dependencies:
- dependency-name: lycheeverse/lychee-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/check-links.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
index bad9c1a6943..ccb056e9bec 100644
--- a/.github/workflows/check-links.yml
+++ b/.github/workflows/check-links.yml
@@ -31,7 +31,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1.9.3
+        uses: lycheeverse/lychee-action@v1.10.0
         with:
           fail: true
           args: --accept '200,201,202,203,204,403,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

From a66e76097070f3763987f29ce1d11fec74af26b3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:09:52 +0000
Subject: [PATCH 21/54] Bump actions/github-script from 6 to 7 (#11265)

Bumps [actions/github-script](https://github.com/actions/github-script) from 6 to 7.
- [Release notes](https://github.com/actions/github-script/releases)
- [Commits](https://github.com/actions/github-script/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/github-script
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 34e34a5086c..9f2625a7228 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -340,7 +340,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - if: github.head_ref == 'main'
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
               core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read https://devdocs.jabref.org/contributing again carefully. 👈')

From 4b1f04b94c190e484927127369ed2b1005c3d8ed Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:25:04 +0000
Subject: [PATCH 22/54] Bump org.xmlunit:xmlunit-matchers from 2.9.1 to 2.10.0
 (#11263)

Bumps [org.xmlunit:xmlunit-matchers](https://github.com/xmlunit/xmlunit) from 2.9.1 to 2.10.0.
- [Release notes](https://github.com/xmlunit/xmlunit/releases)
- [Changelog](https://github.com/xmlunit/xmlunit/blob/main/RELEASE_NOTES.md)
- [Commits](https://github.com/xmlunit/xmlunit/compare/v2.9.1...v2.10.0)

---
updated-dependencies:
- dependency-name: org.xmlunit:xmlunit-matchers
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 77dd961a65c..11ed7431454 100644
--- a/build.gradle
+++ b/build.gradle
@@ -304,7 +304,7 @@ dependencies {
 
     testImplementation 'org.mockito:mockito-core:5.11.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
-    testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
+    testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.3.0'
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"

From 3abdefd5050a291f89ebe47b9c5218750c459348 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 29 Apr 2024 18:32:01 +0200
Subject: [PATCH 23/54] Fix Biodiversity fetcher test results (#11257)

* Fix Biodiversity fetcher test results

* Make CiteSeer test more relaxed when CiteSeer is not available

* Fix CrossRefTest

* Fix import

* "Fix" IEEETest

* Fix ISIDORE Fetcher Test

* Disable ScholarArchiveFetcher

* Disable more tests

* Disable Grobid
---
 .../fetcher/BiodiversityLibraryTest.java      |  2 +-
 .../logic/importer/fetcher/CiteSeerTest.java  |  7 +++
 .../logic/importer/fetcher/CrossRefTest.java  |  1 -
 .../logic/importer/fetcher/IEEETest.java      | 53 +++++++++++++------
 .../importer/fetcher/ISIDOREFetcherTest.java  |  4 +-
 .../fetcher/ScholarArchiveFetcherTest.java    | 18 +++----
 .../importer/fetcher/SemanticScholarTest.java | 17 +++---
 .../fileformat/PdfGrobidImporterTest.java     |  3 ++
 8 files changed, 66 insertions(+), 39 deletions(-)

diff --git a/src/test/java/org/jabref/logic/importer/fetcher/BiodiversityLibraryTest.java b/src/test/java/org/jabref/logic/importer/fetcher/BiodiversityLibraryTest.java
index b5d4fb4f584..b4cf58532f9 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/BiodiversityLibraryTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/BiodiversityLibraryTest.java
@@ -100,7 +100,7 @@ public void performSearch() throws FetcherException {
             .withField(StandardField.URL, "https://www.biodiversitylibrary.org/part/356490")
             .withField(StandardField.DATE, "2023")
             .withField(StandardField.VOLUME, "227")
-            .withField(StandardField.PAGES, "89-97")
+            .withField(StandardField.PAGES, "89--97")
             .withField(StandardField.DOI, "10.3897/phytokeys.227.104703");
 
         assertEquals(expected, fetcher.performSearch("Amanoa condorensis (Phyllanthaceae)").getFirst());
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/CiteSeerTest.java b/src/test/java/org/jabref/logic/importer/fetcher/CiteSeerTest.java
index 647c18d789d..8b5b4f125cd 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/CiteSeerTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/CiteSeerTest.java
@@ -13,18 +13,25 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.testutils.category.FetcherTest;
 
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assumptions.assumeFalse;
 
 @FetcherTest
 class CiteSeerTest {
 
     private CiteSeer fetcher = new CiteSeer();
 
+    @BeforeAll
+    static void ensureCiteSeerIsAvailable() throws Exception {
+        assumeFalse(List.of().equals(new CiteSeer().performSearch("title:\"Rigorous Derivation from Landau-de Gennes Theory to Ericksen-leslie Theory\" AND pageSize:1")));
+    }
+
     @Test
     void searchByQueryFindsEntryRigorousDerivation() throws Exception {
         String title = "RIGOROUS DERIVATION FROM LANDAU-DE GENNES THEORY TO ERICKSEN-LESLIE THEORY";
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java b/src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java
index 287b65e857d..d67744df55d 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java
@@ -132,7 +132,6 @@ public void performSearchByIdFindsPaperWithoutTitle() throws Exception {
         entry.setField(StandardField.JOURNAL, "Indo-Iranian Journal");
         entry.setField(StandardField.NUMBER, "2");
         entry.setField(StandardField.PUBLISHER, "Brill");
-        entry.setField(StandardField.KEYWORDS, "Political Science and International Relations, Linguistics and Language, Philosophy");
 
         assertEquals(Optional.of(entry), fetcher.performSearchById("10.1023/a:1003473214310"));
     }
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/IEEETest.java b/src/test/java/org/jabref/logic/importer/fetcher/IEEETest.java
index 965fde89a1a..eeffcf5aa98 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/IEEETest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/IEEETest.java
@@ -16,18 +16,25 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.testutils.category.FetcherTest;
 
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assumptions.assumeFalse;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
 @FetcherTest
 class IEEETest implements SearchBasedFetcherCapabilityTest, PagedSearchFetcherTest {
 
-    private final BibEntry IGOR_NEWCOMERS = new BibEntry(StandardEntryType.InProceedings)
+    private static ImportFormatPreferences importFormatPreferences;
+
+    private static ImporterPreferences importerPreferences;
+
+    private static final BibEntry IGOR_NEWCOMERS = new BibEntry(StandardEntryType.InProceedings)
             .withField(StandardField.AUTHOR, "Igor Steinmacher and Tayana Uchoa Conte and Christoph Treude and Marco Aurélio Gerosa")
             .withField(StandardField.DATE, "14-22 May 2016")
             .withField(StandardField.YEAR, "2016")
@@ -45,65 +52,76 @@ class IEEETest implements SearchBasedFetcherCapabilityTest, PagedSearchFetcherTe
             .withField(StandardField.FILE, ":https\\://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7886910:PDF");
 
     private IEEE fetcher;
-    private BibEntry entry;
 
-    @BeforeEach
-    void setUp() {
-        ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
+    @BeforeAll
+    static void ensureIeeeIsAvailable() throws Exception {
+        importFormatPreferences = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
         when(importFormatPreferences.bibEntryPreferences().getKeywordSeparator()).thenReturn(',');
 
-        ImporterPreferences importerPreferences = mock(ImporterPreferences.class);
+        importerPreferences = mock(ImporterPreferences.class);
         when(importerPreferences.getApiKeys()).thenReturn(FXCollections.emptyObservableSet());
 
+        IEEE ieee = new IEEE(importFormatPreferences, importerPreferences);
+
+        assumeFalse(List.of().equals(ieee.performSearch("article_number:8801912")));
+    }
+
+    @BeforeEach
+    void setUp() {
         fetcher = new IEEE(importFormatPreferences, importerPreferences);
-        entry = new BibEntry();
     }
 
     @Test
+    @Disabled("IEEE seems to block us")
     void findByDOI() throws Exception {
-        entry.setField(StandardField.DOI, "10.1109/ACCESS.2016.2535486");
+        BibEntry entry = new BibEntry().withField(StandardField.DOI, "10.1109/ACCESS.2016.2535486");
         assertEquals(Optional.of(new URL("https://ieeexplore.ieee.org/ielx7/6287639/7419931/07421926.pdf?tp=&arnumber=7421926&isnumber=7419931&ref=")),
                 fetcher.findFullText(entry));
     }
 
     @Test
+    @Disabled("IEEE seems to block us")
     void findByDocumentUrl() throws Exception {
-        entry.setField(StandardField.URL, "https://ieeexplore.ieee.org/document/7421926/");
+        BibEntry entry = new BibEntry().withField(StandardField.URL, "https://ieeexplore.ieee.org/document/7421926/");
         assertEquals(Optional.of(new URL("https://ieeexplore.ieee.org/ielx7/6287639/7419931/07421926.pdf?tp=&arnumber=7421926&isnumber=7419931&ref=")),
                 fetcher.findFullText(entry));
     }
 
     @Test
+    @Disabled("IEEE seems to block us")
     void findByURL() throws Exception {
-        entry.setField(StandardField.URL, "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7421926&ref=");
+        BibEntry entry = new BibEntry().withField(StandardField.URL, "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7421926&ref=");
         assertEquals(Optional.of(new URL("https://ieeexplore.ieee.org/ielx7/6287639/7419931/07421926.pdf?tp=&arnumber=7421926&isnumber=7419931&ref=")),
                 fetcher.findFullText(entry));
     }
 
     @Test
+    @Disabled("IEEE blocks us - works in browser")
     void findByOldURL() throws Exception {
-        entry.setField(StandardField.URL, "https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7421926");
+        BibEntry entry = new BibEntry().withField(StandardField.URL, "https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7421926");
         assertEquals(Optional.of(new URL("https://ieeexplore.ieee.org/ielx7/6287639/7419931/07421926.pdf?tp=&arnumber=7421926&isnumber=7419931&ref=")),
                 fetcher.findFullText(entry));
     }
 
     @Test
+    @Disabled("IEEE seems to block us")
     void findByDOIButNotURL() throws Exception {
-        entry.setField(StandardField.DOI, "10.1109/ACCESS.2016.2535486");
-        entry.setField(StandardField.URL, "http://dx.doi.org/10.1109/ACCESS.2016.2535486");
+        BibEntry entry = new BibEntry()
+                .withField(StandardField.DOI, "10.1109/ACCESS.2016.2535486")
+                .withField(StandardField.URL, "http://dx.doi.org/10.1109/ACCESS.2016.2535486");
         assertEquals(Optional.of(new URL("https://ieeexplore.ieee.org/ielx7/6287639/7419931/07421926.pdf?tp=&arnumber=7421926&isnumber=7419931&ref=")),
                 fetcher.findFullText(entry));
     }
 
     @Test
     void notFoundByURL() throws Exception {
-        entry.setField(StandardField.URL, "http://dx.doi.org/10.1109/ACCESS.2016.2535486");
+        BibEntry entry = new BibEntry().withField(StandardField.URL, "http://dx.doi.org/10.1109/ACCESS.2016.2535486");
         assertEquals(Optional.empty(), fetcher.findFullText(entry));
     }
 
     @Test
     void notFoundByDOI() throws Exception {
-        entry.setField(StandardField.DOI, "10.1021/bk-2006-WWW.ch014");
+        BibEntry entry = new BibEntry().withField(StandardField.DOI, "10.1021/bk-2006-WWW.ch014");
         assertEquals(Optional.empty(), fetcher.findFullText(entry));
     }
 
@@ -124,8 +142,9 @@ void searchResultHasNoKeywordTerms() throws Exception {
                 .withField(StandardField.VOLUME, "16")
                 .withField(StandardField.KEYWORDS, "Batteries, Generators, Economics, Power quality, State of charge, Harmonic analysis, Control systems, Battery, diesel generator (DG), distributed generation, power quality, photovoltaic (PV), voltage source converter (VSC)");
 
-        List<BibEntry> fetchedEntries = fetcher.performSearch("article_number:8801912"); // article number
-        fetchedEntries.forEach(entry -> entry.clearField(StandardField.ABSTRACT)); // Remove abstract due to copyright);
+        List<BibEntry> fetchedEntries = fetcher.performSearch("article_number:8801912");
+        // Abstract should not be included in JabRef tests (copyrighted)
+        fetchedEntries.forEach(entry -> entry.clearField(StandardField.ABSTRACT));
         assertEquals(Collections.singletonList(expected), fetchedEntries);
     }
 
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/ISIDOREFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/ISIDOREFetcherTest.java
index 1b24ea179c9..6fd5239ce0c 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/ISIDOREFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/ISIDOREFetcherTest.java
@@ -67,8 +67,8 @@ public void checkThesis() throws FetcherException {
 
         List<BibEntry> actual = fetcher.performSearch("Mapping English L2 errors: an integrated system and textual approach");
 
-        // Fetcher returns the same entry twice.
-        assertEquals(List.of(expected, expected), actual);
+        // Fetcher returns the same entry twice. Since 2024, it also returns an additional entry. We just ignore this for now.
+        assertEquals(expected, actual.getFirst());
     }
 
     @Test
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcherTest.java
index 0af2c4f0eb4..3ebe337344c 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcherTest.java
@@ -9,6 +9,7 @@
 import org.jabref.testutils.category.FetcherTest;
 
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -22,16 +23,10 @@ public class ScholarArchiveFetcherTest {
     @BeforeEach
     public void setUp() {
         fetcher = new ScholarArchiveFetcher();
-        bibEntry = new BibEntry(StandardEntryType.InCollection)
-                .withField(StandardField.TITLE, "Query expansion using associated queries")
-                .withField(StandardField.AUTHOR, "Billerbeck, Bodo and Scholer, Falk and Williams, Hugh E. and Zobel, Justin")
-                .withField(StandardField.VOLUME, "0")
-                .withField(StandardField.DOI, "10.1145/956863.956866")
-                .withField(StandardField.JOURNAL, "Proceedings of the twelfth international conference on Information and knowledge management - CIKM '03")
-                .withField(StandardField.PUBLISHER, "ACM Press")
-                .withField(StandardField.TYPE, "paper-conference")
-                .withField(StandardField.YEAR, "2003")
-                .withField(StandardField.URL, "https://web.archive.org/web/20170810164449/http://goanna.cs.rmit.edu.au/~jz/fulltext/cikm03.pdf");
+        bibEntry = new BibEntry(StandardEntryType.InProceedings)
+                .withField(StandardField.TITLE, "BPELscript: A Simplified Script Syntax for WS-BPEL 2.0")
+                .withField(StandardField.AUTHOR, "Marc Bischof and Oliver Kopp and Tammo van Lessen and Frank Leymann ")
+                .withField(StandardField.YEAR, "2009");
     }
 
     @Test
@@ -40,8 +35,9 @@ public void getNameReturnsCorrectName() {
     }
 
     @Test
+    @Disabled("We seem to be blocked")
     public void performSearchReturnsExpectedResults() throws FetcherException {
-        List<BibEntry> fetchedEntries = fetcher.performSearch("query");
+        List<BibEntry> fetchedEntries = fetcher.performSearch("bpelscript");
         fetchedEntries.forEach(entry -> entry.clearField(StandardField.ABSTRACT));
         assertTrue(fetchedEntries.contains(bibEntry), "Found the following entries " + fetchedEntries);
     }
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/SemanticScholarTest.java b/src/test/java/org/jabref/logic/importer/fetcher/SemanticScholarTest.java
index 32045374354..04f53818564 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/SemanticScholarTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/SemanticScholarTest.java
@@ -44,12 +44,10 @@ public class SemanticScholarTest implements PagedSearchFetcherTest {
             .withField(StandardField.VENUE, "International Conference on Software Engineering");
 
     private SemanticScholar fetcher;
-    private BibEntry entry;
 
     @BeforeEach
     void setUp() {
         fetcher = new SemanticScholar(importerPreferences);
-        entry = new BibEntry();
     }
 
     @Test
@@ -64,7 +62,7 @@ void getDocument() throws IOException, FetcherException {
     @Disabled("Returns a DOI instead of the required link")
     @DisabledOnCIServer("CI server is unreliable")
     void fullTextFindByDOI() throws Exception {
-        entry.setField(StandardField.DOI, "10.1038/nrn3241");
+        BibEntry entry = new BibEntry().withField(StandardField.DOI, "10.1038/nrn3241");
         assertEquals(
                 Optional.of(new URI("https://europepmc.org/articles/pmc4907333?pdf=render").toURL()),
                 fetcher.findFullText(entry)
@@ -73,6 +71,7 @@ void fullTextFindByDOI() throws Exception {
 
     @Test
     @DisabledOnCIServer("CI server is unreliable")
+    @Disabled("Sometimes, does not find any thing")
     void fullTextFindByDOIAlternate() throws Exception {
         assertEquals(
                 Optional.of(new URI("https://pdfs.semanticscholar.org/7f6e/61c254bc2df38a784c1228f56c13317caded.pdf").toURL()),
@@ -89,8 +88,8 @@ void fullTextSearchOnEmptyEntry() throws IOException, FetcherException {
     @Test
     @DisabledOnCIServer("CI server is unreliable")
     void fullTextNotFoundByDOI() throws IOException, FetcherException {
-        entry = new BibEntry().withField(StandardField.DOI, DOI);
-        entry.setField(StandardField.DOI, "10.1021/bk-2006-WWW.ch014");
+        BibEntry entry = new BibEntry().withField(StandardField.DOI, DOI)
+                                       .withField(StandardField.DOI, "10.1021/bk-2006-WWW.ch014");
 
         assertEquals(Optional.empty(), fetcher.findFullText(entry));
     }
@@ -98,7 +97,7 @@ void fullTextNotFoundByDOI() throws IOException, FetcherException {
     @Test
     @DisabledOnCIServer("CI server is unreliable")
     void fullTextFindByArXiv() throws Exception {
-        entry = new BibEntry().withField(StandardField.EPRINT, "1407.3561")
+        BibEntry entry = new BibEntry().withField(StandardField.EPRINT, "1407.3561")
                               .withField(StandardField.ARCHIVEPREFIX, "arXiv");
         assertEquals(
                 Optional.of(new URI("https://arxiv.org/pdf/1407.3561.pdf").toURL()),
@@ -130,6 +129,7 @@ void getURLForQueryWithLucene() throws QueryNodeParseException, MalformedURLExce
     }
 
     @Test
+    @Disabled("We seem to be blocked")
     void searchByQueryFindsEntry() throws Exception {
         BibEntry master = new BibEntry(StandardEntryType.Article)
                 .withField(StandardField.AUTHOR, "Tobias Diez")
@@ -145,6 +145,7 @@ void searchByQueryFindsEntry() throws Exception {
     }
 
     @Test
+    @Disabled("We seem to be blocked")
     void searchByPlainQueryFindsEntry() throws Exception {
         List<BibEntry> fetchedEntries = fetcher.performSearch("Overcoming Open Source Project Entry Barriers with a Portal for Newcomers");
         // Abstract should not be included in JabRef tests
@@ -153,6 +154,7 @@ void searchByPlainQueryFindsEntry() throws Exception {
     }
 
     @Test
+    @Disabled("We seem to be blocked")
     void searchByQuotedQueryFindsEntry() throws Exception {
         List<BibEntry> fetchedEntries = fetcher.performSearch("\"Overcoming Open Source Project Entry Barriers with a Portal for Newcomers\"");
         // Abstract should not be included in JabRef tests
@@ -166,6 +168,7 @@ public void performSearchByEmptyQuery() throws Exception {
     }
 
     @Test
+    @Disabled("We seem to be blocked")
     public void findByEntry() throws Exception {
         BibEntry barrosEntry = new BibEntry(StandardEntryType.Article)
                 .withField(StandardField.TITLE, "Formalising BPMN Service Interaction Patterns")
@@ -175,7 +178,7 @@ public void findByEntry() throws Exception {
                 .withField(StandardField.URL, "https://www.semanticscholar.org/paper/3bb026fd67db7d8e0e25de3189d6b7031b12783e")
                 .withField(StandardField.VENUE, "The Practice of Enterprise Modeling");
 
-        entry.withField(StandardField.TITLE, "Formalising BPMN Service Interaction Patterns");
+        BibEntry entry = new BibEntry().withField(StandardField.TITLE, "Formalising BPMN Service Interaction Patterns");
         BibEntry actual = fetcher.performSearch(entry).getFirst();
         // Abstract should not be included in JabRef tests
         actual.clearField(StandardField.ABSTRACT);
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/PdfGrobidImporterTest.java b/src/test/java/org/jabref/logic/importer/fileformat/PdfGrobidImporterTest.java
index 33977668ee3..5f9153434fa 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/PdfGrobidImporterTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/PdfGrobidImporterTest.java
@@ -14,6 +14,7 @@
 import org.jabref.testutils.category.FetcherTest;
 
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.mockito.Answers;
 
@@ -47,10 +48,12 @@ public void getExtensions() {
     }
 
     @Test
+    @Disabled("Currently does not return anything")
     public void importEntries() throws URISyntaxException {
         Path file = Path.of(PdfGrobidImporterTest.class.getResource("LNCS-minimal.pdf").toURI());
         List<BibEntry> bibEntries = importer.importDatabase(file).getDatabase().getEntries();
 
+        // TODO: Rewrite using our logic of full BibEntries
         assertEquals(1, bibEntries.size());
 
         BibEntry be0 = bibEntries.getFirst();

From 4f877400c57953feefb4ea77adc14c35ede5613b Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Tue, 30 Apr 2024 09:05:56 +0300
Subject: [PATCH 24/54] Update search results when active database changes
 (#11268)

Merged origin/update-search-results into update-search-results
---
 src/main/java/org/jabref/gui/search/GlobalSearchBar.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
index de9319c93a3..5c18e02243a 100644
--- a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
+++ b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
@@ -238,7 +238,7 @@ public GlobalSearchBar(LibraryTabContainer tabContainer,
                 query -> setSearchTerm(query.map(SearchQuery::getQuery).orElse("")));
 
         this.searchQueryProperty.addListener((obs, oldValue, newValue) -> newValue.ifPresent(this::updateSearchResultsForQuery));
-        this.searchQueryProperty.addListener((obs, oldValue, newValue) -> searchQueryProperty.get().ifPresent(this::updateSearchResultsForQuery));
+        this.stateManager.activeDatabaseProperty().addListener(obs -> searchQueryProperty.get().ifPresent(this::updateSearchResultsForQuery));
         /*
          * The listener tracks a change on the focus property value.
          * This happens, from active (user types a query) to inactive / focus

From dc5b413fd875da5bc37d3a5bfccb2ac6819bcebc Mon Sep 17 00:00:00 2001
From: HoussemNasri <houssemnasri2001@gmail.com>
Date: Tue, 30 Apr 2024 12:31:58 +0100
Subject: [PATCH 25/54] Fix drag and dropping entries not always working

- It doesn't work if the destination library has no group structure; "All entries" is the only group.
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/frame/FrameDndHandler.java | 75 ++++++++++++-------
 2 files changed, 49 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99fc9dfa8fa..c1e90236059 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed crash on opening the entry editor when auto completion is enabled. [#11188](https://github.com/JabRef/jabref/issues/11188)
 - We fixed the usage of the key binding for "Clear search" (default: <kbd>Escape</kbd>). [#10764](https://github.com/JabRef/jabref/issues/10764)
 - We fixed an issue where library shown as unsaved and marked (*) after accepting changes made externally to the file. [#11027](https://github.com/JabRef/jabref/issues/11027)
+- We fixed an issue where drag and dropping entries from one library to another was not always working. [#11254](https://github.com/JabRef/jabref/issues/11254)
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/frame/FrameDndHandler.java b/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
index 75fd0aebb77..a065870cbe5 100644
--- a/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
+++ b/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
@@ -26,8 +26,12 @@
 import org.jabref.model.groups.GroupTreeNode;
 
 import com.tobiasdiez.easybind.EasyBind;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class FrameDndHandler {
+    private static final Logger LOGGER = LoggerFactory.getLogger(FrameDndHandler.class);
+
     private final TabPane tabPane;
     private final Supplier<Scene> scene;
     private final Supplier<OpenDatabaseAction> openDatabaseAction;
@@ -81,45 +85,62 @@ private void onTabDragDropped(Node destinationTabNode, DragEvent tabDragEvent, T
             tabDragEvent.setDropCompleted(true);
             tabDragEvent.consume();
         } else {
-            if (stateManager.getActiveDatabase().isEmpty()
-                || stateManager.getActiveDatabase().get().getMetaData().getGroups().isEmpty()) {
+            if (stateManager.getActiveDatabase().isEmpty()) {
+                LOGGER.warn("Active library is empty when dropping entries");
                 return;
             }
 
+            LibraryTab destinationLibraryTab = null;
             for (Tab libraryTab : tabPane.getTabs()) {
                 if (libraryTab.getId().equals(destinationTabNode.getId()) &&
                         !tabPane.getSelectionModel().getSelectedItem().equals(libraryTab)) {
-                    LibraryTab destinationLibraryTab = (LibraryTab) libraryTab;
-                    if (hasGroups(dragboard)) {
-                        List<String> groupPathToSources = getGroups(dragboard);
-
-                        copyRootNode(destinationLibraryTab);
-
-                        GroupTreeNode destinationLibraryGroupRoot = destinationLibraryTab
-                                .getBibDatabaseContext()
-                                .getMetaData()
-                                .getGroups().get();
-
-                        GroupTreeNode groupsTreeNode = stateManager.getActiveDatabase().get()
-                                                                   .getMetaData()
-                                                                   .getGroups()
-                                                                   .get();
-
-                        for (String pathToSource : groupPathToSources) {
-                            GroupTreeNode groupTreeNodeToCopy = groupsTreeNode
-                                    .getChildByPath(pathToSource)
-                                    .get();
-                            copyGroupTreeNode((LibraryTab) libraryTab, destinationLibraryGroupRoot, groupTreeNodeToCopy);
-                        }
-                        return;
-                    }
-                    destinationLibraryTab.dropEntry(stateManager.getLocalDragboard().getBibEntries());
+                    destinationLibraryTab = (LibraryTab) libraryTab;
+                    break;
                 }
             }
+
+            if (destinationLibraryTab == null) {
+                LOGGER.warn("Failed to find library tab to drop into");
+                return;
+            }
+
+            if (hasEntries(dragboard)) {
+                destinationLibraryTab.dropEntry(stateManager.getLocalDragboard().getBibEntries());
+            } else if (hasGroups(dragboard)) {
+                dropGroups(dragboard, destinationLibraryTab);
+            }
+
             tabDragEvent.consume();
         }
     }
 
+    private void dropGroups(Dragboard dragboard, LibraryTab destinationLibraryTab) {
+        List<String> groupPathToSources = getGroups(dragboard);
+
+        copyRootNode(destinationLibraryTab);
+
+        GroupTreeNode destinationLibraryGroupRoot = destinationLibraryTab
+                .getBibDatabaseContext()
+                .getMetaData()
+                .getGroups().get();
+
+        GroupTreeNode groupsTreeNode = stateManager.getActiveDatabase().get()
+                                                   .getMetaData()
+                                                   .getGroups()
+                                                   .get();
+
+        for (String pathToSource : groupPathToSources) {
+            GroupTreeNode groupTreeNodeToCopy = groupsTreeNode
+                    .getChildByPath(pathToSource)
+                    .get();
+            copyGroupTreeNode(destinationLibraryTab, destinationLibraryGroupRoot, groupTreeNodeToCopy);
+        }
+    }
+
+    private boolean hasEntries(Dragboard dragboard) {
+        return dragboard.hasContent(DragAndDropDataFormats.ENTRIES);
+    }
+
     private void onTabDragOver(DragEvent event, DragEvent tabDragEvent, Tab dndIndicator) {
         if (hasBibFiles(tabDragEvent.getDragboard()) || hasGroups(tabDragEvent.getDragboard())) {
             tabDragEvent.acceptTransferModes(TransferMode.ANY);

From 9f259c9c22e570ab33b2f45d608add1e064b1391 Mon Sep 17 00:00:00 2001
From: HoussemNasri <houssemnasri2001@gmail.com>
Date: Tue, 30 Apr 2024 12:34:34 +0100
Subject: [PATCH 26/54] Fix drag and dropping entries create a shallow copy

---
 CHANGELOG.md                                            | 1 +
 src/main/java/org/jabref/gui/frame/FrameDndHandler.java | 5 ++++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1e90236059..4e3a4c875e6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed the usage of the key binding for "Clear search" (default: <kbd>Escape</kbd>). [#10764](https://github.com/JabRef/jabref/issues/10764)
 - We fixed an issue where library shown as unsaved and marked (*) after accepting changes made externally to the file. [#11027](https://github.com/JabRef/jabref/issues/11027)
 - We fixed an issue where drag and dropping entries from one library to another was not always working. [#11254](https://github.com/JabRef/jabref/issues/11254)
+- We fixed an issue where drag and dropping entries created a shallow copy. [#11160](https://github.com/JabRef/jabref/issues/11160)
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/frame/FrameDndHandler.java b/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
index a065870cbe5..424b3512488 100644
--- a/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
+++ b/src/main/java/org/jabref/gui/frame/FrameDndHandler.java
@@ -105,7 +105,10 @@ private void onTabDragDropped(Node destinationTabNode, DragEvent tabDragEvent, T
             }
 
             if (hasEntries(dragboard)) {
-                destinationLibraryTab.dropEntry(stateManager.getLocalDragboard().getBibEntries());
+                List<BibEntry> entryCopies = stateManager.getLocalDragboard().getBibEntries()
+                                                         .stream().map(entry -> (BibEntry) entry.clone())
+                                                         .toList();
+                destinationLibraryTab.dropEntry(entryCopies);
             } else if (hasGroups(dragboard)) {
                 dropGroups(dragboard, destinationLibraryTab);
             }

From ca16e86dd8bb16b7051bd1f0b8ff615acdf36524 Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Thu, 2 May 2024 11:31:23 +0200
Subject: [PATCH 27/54] Fix import selected groups (#11271)

* Fix import entries to custom groups only working for one entry

* changelog

* rename getSelectedGroups, prefix  uid
add changelog entries
---
 CHANGELOG.md                                  |  2 ++
 src/main/java/org/jabref/gui/LibraryTab.java  |  4 +++-
 .../java/org/jabref/gui/StateManager.java     | 14 +++++------
 .../gui/externalfiles/ImportHandler.java      |  2 +-
 .../jabref/gui/groups/GroupNodeViewModel.java |  2 +-
 .../jabref/gui/groups/GroupTreeViewModel.java |  4 ++--
 .../model/database/BibDatabaseContext.java    | 24 +++++++++++++++----
 .../gui/groups/GroupTreeViewModelTest.java    |  2 +-
 8 files changed, 37 insertions(+), 17 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4a9bb0871b9..410b5341a73 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where library shown as unsaved and marked (*) after accepting changes made externally to the file. [#11027](https://github.com/JabRef/jabref/issues/11027)
 - We fixed an issue where drag and dropping entries from one library to another was not always working. [#11254](https://github.com/JabRef/jabref/issues/11254)
 - We fixed an issue where drag and dropping entries created a shallow copy. [#11160](https://github.com/JabRef/jabref/issues/11160)
+- We fixed an issue where imports to a custom group would only work for the first entry [#11085](https://github.com/JabRef/jabref/issues/11085), [#11269](https://github.com/JabRef/jabref/issues/11269)
+- We fixed an issue where a new entry was not added to the selected group [#8933](https://github.com/JabRef/jabref/issues/8933)
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
index 02ee691c747..ff2c9e4ba20 100644
--- a/src/main/java/org/jabref/gui/LibraryTab.java
+++ b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -857,6 +857,8 @@ private void onClosed(Event event) {
         } catch (RuntimeException e) {
             LOGGER.error("Problem when shutting down backup manager", e);
         }
+        // clean up the groups map
+        stateManager.clearSelectedGroups(bibDatabaseContext);
     }
 
     /**
@@ -1033,7 +1035,7 @@ public void listen(EntriesAddedEvent addedEntriesEvent) {
 
             // Automatically add new entries to the selected group (or set of groups)
             if (preferencesService.getGroupsPreferences().shouldAutoAssignGroup()) {
-                stateManager.getSelectedGroup(bibDatabaseContext).forEach(
+                stateManager.getSelectedGroups(bibDatabaseContext).forEach(
                         selectedGroup -> selectedGroup.addEntriesToGroup(addedEntriesEvent.getBibEntries()));
             }
         }
diff --git a/src/main/java/org/jabref/gui/StateManager.java b/src/main/java/org/jabref/gui/StateManager.java
index 010375fc1c5..9513c3fe3f1 100644
--- a/src/main/java/org/jabref/gui/StateManager.java
+++ b/src/main/java/org/jabref/gui/StateManager.java
@@ -57,13 +57,13 @@ public class StateManager {
     private final OptionalObjectProperty<LibraryTab> activeTab = OptionalObjectProperty.empty();
     private final ReadOnlyListWrapper<GroupTreeNode> activeGroups = new ReadOnlyListWrapper<>(FXCollections.observableArrayList());
     private final ObservableList<BibEntry> selectedEntries = FXCollections.observableArrayList();
-    private final ObservableMap<BibDatabaseContext, ObservableList<GroupTreeNode>> selectedGroups = FXCollections.observableHashMap();
+    private final ObservableMap<String, ObservableList<GroupTreeNode>> selectedGroups = FXCollections.observableHashMap();
     private final OptionalObjectProperty<SearchQuery> activeSearchQuery = OptionalObjectProperty.empty();
     private final OptionalObjectProperty<SearchQuery> activeGlobalSearchQuery = OptionalObjectProperty.empty();
     private final IntegerProperty globalSearchResultSize = new SimpleIntegerProperty(0);
     private final ObservableMap<BibDatabaseContext, IntegerProperty> searchResultMap = FXCollections.observableHashMap();
     private final OptionalObjectProperty<Node> focusOwner = OptionalObjectProperty.empty();
-    private final ObservableList<Pair<BackgroundTask<?>, Task<?>>> backgroundTasks = FXCollections.observableArrayList(task -> new Observable[]{task.getValue().progressProperty(), task.getValue().runningProperty()});
+    private final ObservableList<Pair<BackgroundTask<?>, Task<?>>> backgroundTasks = FXCollections.observableArrayList(task -> new Observable[] {task.getValue().progressProperty(), task.getValue().runningProperty()});
     private final EasyBinding<Boolean> anyTaskRunning = EasyBind.reduce(backgroundTasks, tasks -> tasks.map(Pair::getValue).anyMatch(Task::isRunning));
     private final EasyBinding<Boolean> anyTasksThatWillNotBeRecoveredRunning = EasyBind.reduce(backgroundTasks, tasks -> tasks.anyMatch(task -> !task.getKey().willBeRecoveredAutomatically() && task.getValue().isRunning()));
     private final EasyBinding<Double> tasksProgress = EasyBind.reduce(backgroundTasks, tasks -> tasks.map(Pair::getValue).filter(Task::isRunning).mapToDouble(Task::getProgress).average().orElse(1));
@@ -75,7 +75,7 @@ public class StateManager {
     private final ObservableList<String> searchHistory = FXCollections.observableArrayList();
 
     public StateManager() {
-        activeGroups.bind(Bindings.valueAt(selectedGroups, activeDatabase.orElseOpt(null)));
+        activeGroups.bind(Bindings.valueAt(selectedGroups, activeDatabase.orElseOpt(null).map(BibDatabaseContext::getUid)));
     }
 
     public ObservableList<SidePaneType> getVisibleSidePaneComponents() {
@@ -140,16 +140,16 @@ public void setSelectedEntries(List<BibEntry> newSelectedEntries) {
 
     public void setSelectedGroups(BibDatabaseContext database, List<GroupTreeNode> newSelectedGroups) {
         Objects.requireNonNull(newSelectedGroups);
-        selectedGroups.put(database, FXCollections.observableArrayList(newSelectedGroups));
+        selectedGroups.put(database.getUid(), FXCollections.observableArrayList(newSelectedGroups));
     }
 
-    public ObservableList<GroupTreeNode> getSelectedGroup(BibDatabaseContext database) {
-        ObservableList<GroupTreeNode> selectedGroupsForDatabase = selectedGroups.get(database);
+    public ObservableList<GroupTreeNode> getSelectedGroups(BibDatabaseContext context) {
+        ObservableList<GroupTreeNode> selectedGroupsForDatabase = selectedGroups.get(context.getUid());
         return selectedGroupsForDatabase != null ? selectedGroupsForDatabase : FXCollections.observableArrayList();
     }
 
     public void clearSelectedGroups(BibDatabaseContext database) {
-        selectedGroups.remove(database);
+        selectedGroups.remove(database.getUid());
     }
 
     public Optional<BibDatabaseContext> getActiveDatabase() {
diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
index 8465c4305f6..96ad7e46e4d 100644
--- a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -194,7 +194,7 @@ public void importCleanedEntries(List<BibEntry> entries) {
         bibDatabaseContext.getDatabase().insertEntries(entries);
         generateKeys(entries);
         setAutomaticFields(entries);
-        addToGroups(entries, stateManager.getSelectedGroup(bibDatabaseContext));
+        addToGroups(entries, stateManager.getSelectedGroups(bibDatabaseContext));
     }
 
     public void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext, BibEntry entry) {
diff --git a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
index bd113bf249e..dccd1fef498 100644
--- a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
@@ -262,7 +262,7 @@ private void refreshGroup() {
         DefaultTaskExecutor.runInJavaFXThread(() -> {
             updateMatchedEntries(); // Update the entries matched by the group
             // "Re-add" to the selected groups if it were selected, this refreshes the entries the user views
-            ObservableList<GroupTreeNode> selectedGroups = this.stateManager.getSelectedGroup(this.databaseContext);
+            ObservableList<GroupTreeNode> selectedGroups = this.stateManager.getSelectedGroups(this.databaseContext);
             if (selectedGroups.remove(this.groupNode)) {
                 selectedGroups.add(this.groupNode);
             }
diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
index 4efab42033b..de0c579699b 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
@@ -153,11 +153,11 @@ private void onActiveDatabaseChanged(Optional<BibDatabaseContext> newDatabase) {
                     .orElse(GroupNodeViewModel.getAllEntriesGroup(newDatabase.get(), stateManager, taskExecutor, localDragboard, preferences));
 
             rootGroup.setValue(newRoot);
-            if (stateManager.getSelectedGroup(newDatabase.get()).isEmpty()) {
+            if (stateManager.getSelectedGroups(newDatabase.get()).isEmpty()) {
                 stateManager.setSelectedGroups(newDatabase.get(), Collections.singletonList(newRoot.getGroupNode()));
             }
             selectedGroups.setAll(
-                    stateManager.getSelectedGroup(newDatabase.get()).stream()
+                    stateManager.getSelectedGroups(newDatabase.get()).stream()
                                 .map(selectedGroup -> new GroupNodeViewModel(newDatabase.get(), stateManager, taskExecutor, selectedGroup, localDragboard, preferences))
                                 .collect(Collectors.toList()));
         } else {
diff --git a/src/main/java/org/jabref/model/database/BibDatabaseContext.java b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
index b43f7069a24..f8d4c3dfdcf 100644
--- a/src/main/java/org/jabref/model/database/BibDatabaseContext.java
+++ b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
@@ -6,6 +6,7 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.UUID;
 import java.util.stream.Collectors;
 
 import org.jabref.architecture.AllowedToUseLogic;
@@ -33,7 +34,7 @@
  * and the options relevant for this file in Defaults.
  * </p>
  * <p>
- *     To get an instance for a .bib file, use {@link org.jabref.logic.importer.fileformat.BibtexParser}.
+ * To get an instance for a .bib file, use {@link org.jabref.logic.importer.fileformat.BibtexParser}.
  * </p>
  */
 @AllowedToUseLogic("because it needs access to shared database features")
@@ -44,6 +45,12 @@ public class BibDatabaseContext {
     private final BibDatabase database;
     private MetaData metaData;
 
+    /**
+     * Generate a random UID for unique of the concrete context
+     * In contrast to hashCode this stays unique
+     */
+    private final String uid = "bibdatabasecontext_" + UUID.randomUUID();
+
     /**
      * The path where this database was last saved to.
      */
@@ -127,9 +134,9 @@ public boolean isBiblatexMode() {
      */
     public boolean isStudy() {
         return this.getDatabasePath()
-                .map(path -> path.getFileName().toString().equals(Crawler.FILENAME_STUDY_RESULT_BIB) &&
-                        Files.exists(path.resolveSibling(StudyRepository.STUDY_DEFINITION_FILE_NAME)))
-                .orElse(false);
+                   .map(path -> path.getFileName().toString().equals(Crawler.FILENAME_STUDY_RESULT_BIB) &&
+                           Files.exists(path.resolveSibling(StudyRepository.STUDY_DEFINITION_FILE_NAME)))
+                   .orElse(false);
     }
 
     /**
@@ -286,4 +293,13 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(database, metaData, path, location);
     }
+
+    /**
+     * Get the generated UID for the current context. Can be used to distinguish contexts with changing metadata etc
+     *
+     * @return The generated UID in UUIDv4 format with the prefix bibdatabasecontext_
+     */
+    public String getUid() {
+        return uid;
+    }
 }
diff --git a/src/test/java/org/jabref/gui/groups/GroupTreeViewModelTest.java b/src/test/java/org/jabref/gui/groups/GroupTreeViewModelTest.java
index 5f7f2369134..bdb27ee2fc1 100644
--- a/src/test/java/org/jabref/gui/groups/GroupTreeViewModelTest.java
+++ b/src/test/java/org/jabref/gui/groups/GroupTreeViewModelTest.java
@@ -61,7 +61,7 @@ void rootGroupIsAllEntriesByDefault() {
 
     @Test
     void rootGroupIsSelectedByDefault() {
-        assertEquals(groupTree.rootGroupProperty().get().getGroupNode(), stateManager.getSelectedGroup(databaseContext).getFirst());
+        assertEquals(groupTree.rootGroupProperty().get().getGroupNode(), stateManager.getSelectedGroups(databaseContext).getFirst());
     }
 
     @Test

From 43e77cbec268e33633db184e2e68e6a7921b30c6 Mon Sep 17 00:00:00 2001
From: compf <timo.schoemaker97@outlook.de>
Date: Fri, 3 May 2024 09:35:40 +0200
Subject: [PATCH 28/54] Refactored data clumps with the help of LLMs (research
 project) (#11181)

* refactored a data clump

* made DocumentAnnotation a record and moved comments

* fixed checkstyle errors

* fixed more checkstyle violatopns

* removed fully qualified name

* fixed documentation and naming issues

---------

Co-authored-by: tschoemaker <=>
---
 .../backend/NamedRangeReferenceMark.java      |  5 +++--
 .../frontend/UpdateBibliography.java          |  7 +++++--
 .../model/openoffice/DocumentAnnotation.java  | 15 +++++++++++++++
 .../model/openoffice/uno/UnoBookmark.java     |  9 ++++-----
 .../jabref/model/openoffice/uno/UnoNamed.java | 19 ++++++-------------
 .../openoffice/uno/UnoReferenceMark.java      | 10 +++++-----
 .../model/openoffice/uno/UnoTextSection.java  | 12 +++++-------
 7 files changed, 43 insertions(+), 34 deletions(-)
 create mode 100644 src/main/java/org/jabref/model/openoffice/DocumentAnnotation.java

diff --git a/src/main/java/org/jabref/logic/openoffice/backend/NamedRangeReferenceMark.java b/src/main/java/org/jabref/logic/openoffice/backend/NamedRangeReferenceMark.java
index 851b084b866..6683a67637a 100644
--- a/src/main/java/org/jabref/logic/openoffice/backend/NamedRangeReferenceMark.java
+++ b/src/main/java/org/jabref/logic/openoffice/backend/NamedRangeReferenceMark.java
@@ -2,6 +2,7 @@
 
 import java.util.Optional;
 
+import org.jabref.model.openoffice.DocumentAnnotation;
 import org.jabref.model.openoffice.backend.NamedRange;
 import org.jabref.model.openoffice.uno.CreationException;
 import org.jabref.model.openoffice.uno.NoDocumentException;
@@ -101,8 +102,8 @@ private static void createReprInDocument(XTextDocument doc,
                 : left + right;
 
         cursor.getText().insertString(cursor, bracketedContent, true);
-
-        UnoReferenceMark.create(doc, refMarkName, cursor, true /* absorb */);
+        DocumentAnnotation documentAnnotation = new DocumentAnnotation(doc, refMarkName, cursor, true /* absorb */);
+        UnoReferenceMark.create(documentAnnotation);
 
         // eat the first inserted space
         cursorBefore.goRight((short) 1, true);
diff --git a/src/main/java/org/jabref/logic/openoffice/frontend/UpdateBibliography.java b/src/main/java/org/jabref/logic/openoffice/frontend/UpdateBibliography.java
index 99e71e13725..47e63414c78 100644
--- a/src/main/java/org/jabref/logic/openoffice/frontend/UpdateBibliography.java
+++ b/src/main/java/org/jabref/logic/openoffice/frontend/UpdateBibliography.java
@@ -4,6 +4,7 @@
 
 import org.jabref.logic.openoffice.style.OOBibStyle;
 import org.jabref.logic.openoffice.style.OOFormatBibliography;
+import org.jabref.model.openoffice.DocumentAnnotation;
 import org.jabref.model.openoffice.ootext.OOText;
 import org.jabref.model.openoffice.ootext.OOTextIntoOO;
 import org.jabref.model.openoffice.style.CitedKeys;
@@ -67,7 +68,8 @@ private static void createBibTextSection2(XTextDocument doc)
         // Alternatively, we could receive a cursor.
         XTextCursor textCursor = doc.getText().createTextCursor();
         textCursor.gotoEnd(false);
-        UnoTextSection.create(doc, BIB_SECTION_NAME, textCursor, false);
+        DocumentAnnotation annotation = new DocumentAnnotation(doc, BIB_SECTION_NAME, textCursor, false);
+        UnoTextSection.create(annotation);
     }
 
     /**
@@ -129,7 +131,8 @@ private static void populateBibTextSection(XTextDocument doc,
         initialParagraph.setString("");
 
         UnoBookmark.removeIfExists(doc, BIB_SECTION_END_NAME);
-        UnoBookmark.create(doc, BIB_SECTION_END_NAME, cursor, true);
+        DocumentAnnotation documentAnnotation = new DocumentAnnotation(doc, BIB_SECTION_END_NAME, cursor, true);
+        UnoBookmark.create(documentAnnotation);
 
         cursor.collapseToEnd();
     }
diff --git a/src/main/java/org/jabref/model/openoffice/DocumentAnnotation.java b/src/main/java/org/jabref/model/openoffice/DocumentAnnotation.java
new file mode 100644
index 00000000000..2d7037f7199
--- /dev/null
+++ b/src/main/java/org/jabref/model/openoffice/DocumentAnnotation.java
@@ -0,0 +1,15 @@
+package org.jabref.model.openoffice;
+
+import com.sun.star.text.XTextDocument;
+import com.sun.star.text.XTextRange;
+
+/**
+ * Represents a document annotation.
+ *
+ * @param doc    The document
+ * @param name   For the ReferenceMark, Bookmark, TextSection. If the name is already in use, LibreOffice may change the name.
+ * @param range  Cursor marking the location or range for the thing to be inserted.
+ * @param absorb ReferenceMark, Bookmark and TextSection can incorporate a text range. If absorb is true, the text in the range becomes part of the thing. If absorb is false, the thing is inserted at the end of the range.
+ */
+public record DocumentAnnotation(XTextDocument doc, String name, XTextRange range, boolean absorb) {
+}
diff --git a/src/main/java/org/jabref/model/openoffice/uno/UnoBookmark.java b/src/main/java/org/jabref/model/openoffice/uno/UnoBookmark.java
index 5f4f5ea40d7..0f87ddcd21b 100644
--- a/src/main/java/org/jabref/model/openoffice/uno/UnoBookmark.java
+++ b/src/main/java/org/jabref/model/openoffice/uno/UnoBookmark.java
@@ -2,6 +2,8 @@
 
 import java.util.Optional;
 
+import org.jabref.model.openoffice.DocumentAnnotation;
+
 import com.sun.star.container.NoSuchElementException;
 import com.sun.star.container.XNameAccess;
 import com.sun.star.container.XNamed;
@@ -52,16 +54,13 @@ public static Optional<XTextRange> getAnchor(XTextDocument doc, String name)
      * <p>
      * In LibreOffice the another name is in "{name}{number}" format.
      *
-     * @param name   For the bookmark.
-     * @param range  Cursor marking the location or range for the bookmark.
-     * @param absorb Shall we incorporate range?
      * @return The XNamed interface of the bookmark.
      * result.getName() should be checked by the caller, because its name may differ from the one requested.
      */
-    public static XNamed create(XTextDocument doc, String name, XTextRange range, boolean absorb)
+    public static XNamed create(DocumentAnnotation documentAnnotation)
             throws
             CreationException {
-        return UnoNamed.insertNamedTextContent(doc, "com.sun.star.text.Bookmark", name, range, absorb);
+        return UnoNamed.insertNamedTextContent("com.sun.star.text.Bookmark", documentAnnotation);
     }
 
     /**
diff --git a/src/main/java/org/jabref/model/openoffice/uno/UnoNamed.java b/src/main/java/org/jabref/model/openoffice/uno/UnoNamed.java
index d3bf46668d1..3352150ba85 100644
--- a/src/main/java/org/jabref/model/openoffice/uno/UnoNamed.java
+++ b/src/main/java/org/jabref/model/openoffice/uno/UnoNamed.java
@@ -1,10 +1,10 @@
 package org.jabref.model.openoffice.uno;
 
+import org.jabref.model.openoffice.DocumentAnnotation;
+
 import com.sun.star.container.XNamed;
 import com.sun.star.lang.XMultiServiceFactory;
 import com.sun.star.text.XTextContent;
-import com.sun.star.text.XTextDocument;
-import com.sun.star.text.XTextRange;
 
 public class UnoNamed {
 
@@ -17,20 +17,13 @@ private UnoNamed() {
      * @param service For example "com.sun.star.text.ReferenceMark", "com.sun.star.text.Bookmark" or "com.sun.star.text.TextSection".
      *                <p>
      *                Passed to this.asXMultiServiceFactory().createInstance(service) The result is expected to support the XNamed and XTextContent interfaces.
-     * @param name    For the ReferenceMark, Bookmark, TextSection. If the name is already in use, LibreOffice may change the name.
-     * @param range   Marks the location or range for the thing to be inserted.
-     * @param absorb  ReferenceMark, Bookmark and TextSection can incorporate a text range. If absorb is true, the text in the range becomes part of the thing. If absorb is false, the thing is inserted at the end of the range.
      * @return The XNamed interface, in case we need to check the actual name.
      */
-    static XNamed insertNamedTextContent(XTextDocument doc,
-                                         String service,
-                                         String name,
-                                         XTextRange range,
-                                         boolean absorb)
+    static XNamed insertNamedTextContent(String service, DocumentAnnotation documentAnnotation)
             throws
             CreationException {
 
-        XMultiServiceFactory msf = UnoCast.cast(XMultiServiceFactory.class, doc).get();
+        XMultiServiceFactory msf = UnoCast.cast(XMultiServiceFactory.class, documentAnnotation.doc()).get();
 
         Object xObject;
         try {
@@ -41,12 +34,12 @@ static XNamed insertNamedTextContent(XTextDocument doc,
 
         XNamed xNamed = UnoCast.cast(XNamed.class, xObject)
                                 .orElseThrow(() -> new IllegalArgumentException("Service is not an XNamed"));
-        xNamed.setName(name);
+        xNamed.setName(documentAnnotation.name());
 
         // get XTextContent interface
         XTextContent xTextContent = UnoCast.cast(XTextContent.class, xObject)
                                             .orElseThrow(() -> new IllegalArgumentException("Service is not an XTextContent"));
-        range.getText().insertTextContent(range, xTextContent, absorb);
+        documentAnnotation.range().getText().insertTextContent(documentAnnotation.range(), xTextContent, documentAnnotation.absorb());
         return xNamed;
     }
 }
diff --git a/src/main/java/org/jabref/model/openoffice/uno/UnoReferenceMark.java b/src/main/java/org/jabref/model/openoffice/uno/UnoReferenceMark.java
index 12e36fae46a..0b9f2adc6c0 100644
--- a/src/main/java/org/jabref/model/openoffice/uno/UnoReferenceMark.java
+++ b/src/main/java/org/jabref/model/openoffice/uno/UnoReferenceMark.java
@@ -5,6 +5,8 @@
 import java.util.List;
 import java.util.Optional;
 
+import org.jabref.model.openoffice.DocumentAnnotation;
+
 import com.sun.star.container.NoSuchElementException;
 import com.sun.star.container.XNameAccess;
 import com.sun.star.container.XNamed;
@@ -105,16 +107,14 @@ public static Optional<XTextRange> getAnchor(XTextDocument doc, String name)
     /**
      * Insert a new reference mark at the provided cursor position.
      * <p>
-     * If {@code absorb} is true, the text in the cursor range will become the text with gray background.
+     * If {@code documentAnnotation.getAbsorb} is true, the text in the cursor range will become the text with gray background.
      * <p>
      * Note: LibreOffice 6.4.6.2 will create multiple reference marks with the same name without error or renaming. Its GUI does not allow this, but we can create them programmatically. In the GUI, clicking on any of those identical names will move the cursor to the same mark.
      *
-     * @param name  For the reference mark.
-     * @param range Cursor marking the location or range for the reference mark.
      */
-    public static XNamed create(XTextDocument doc, String name, XTextRange range, boolean absorb)
+    public static XNamed create(DocumentAnnotation documentAnnotation)
             throws
             CreationException {
-        return UnoNamed.insertNamedTextContent(doc, "com.sun.star.text.ReferenceMark", name, range, absorb);
+        return UnoNamed.insertNamedTextContent("com.sun.star.text.ReferenceMark", documentAnnotation);
     }
 }
diff --git a/src/main/java/org/jabref/model/openoffice/uno/UnoTextSection.java b/src/main/java/org/jabref/model/openoffice/uno/UnoTextSection.java
index 1717795cfa7..9e0c3fddf2d 100644
--- a/src/main/java/org/jabref/model/openoffice/uno/UnoTextSection.java
+++ b/src/main/java/org/jabref/model/openoffice/uno/UnoTextSection.java
@@ -2,6 +2,8 @@
 
 import java.util.Optional;
 
+import org.jabref.model.openoffice.DocumentAnnotation;
+
 import com.sun.star.container.NoSuchElementException;
 import com.sun.star.container.XNameAccess;
 import com.sun.star.container.XNamed;
@@ -63,17 +65,13 @@ public static Optional<XTextRange> getAnchor(XTextDocument doc, String name)
 
     /**
      * Create a text section with the provided name and insert it at the provided cursor.
-     *
-     * @param name  The desired name for the section.
-     * @param range The location to insert at.
-     *              <p>
-     *              If an XTextSection by that name already exists, LibreOffice (6.4.6.2) creates a section with a name different from what we requested, in "Section {number}" format.
+     * If an XTextSection by that name already exists, LibreOffice (6.4.6.2) creates a section with a name different from what we requested, in "Section {number}" format
      */
-    public static XNamed create(XTextDocument doc, String name, XTextRange range, boolean absorb)
+    public static XNamed create(DocumentAnnotation documentAnnotation)
             throws
             CreationException {
 
-        return UnoNamed.insertNamedTextContent(doc, "com.sun.star.text.TextSection", name, range, absorb);
+        return UnoNamed.insertNamedTextContent("com.sun.star.text.TextSection", documentAnnotation);
     }
 }
 

From b4c4d4f1872fd8e695e52d945dedfa2f540df64a Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Fri, 3 May 2024 20:14:00 +0200
Subject: [PATCH 29/54] Update codesign action due to Node 16 deprecation
 (#11266)

* Update deployment-arm64.yml

* Update deployment-jdk-ea.yml

* Update deployment.yml

* Use hash instead of version

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
---
 .github/workflows/deployment-arm64.yml  | 4 ++--
 .github/workflows/deployment-jdk-ea.yml | 4 ++--
 .github/workflows/deployment.yml        | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
index 69c4ac284a5..01675246e2b 100644
--- a/.github/workflows/deployment-arm64.yml
+++ b/.github/workflows/deployment-arm64.yml
@@ -82,14 +82,14 @@ jobs:
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
       - name: Setup OSX key chain on macOS-arm
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup OSX key chain on OSX for app id cert
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
index 340a566df64..63d8e2a1dd5 100644
--- a/.github/workflows/deployment-jdk-ea.yml
+++ b/.github/workflows/deployment-jdk-ea.yml
@@ -200,14 +200,14 @@ jobs:
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Set up macOS key chain
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Set up macOS key chain for app id cert
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index c61282d61c0..0fe694d2a30 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -100,14 +100,14 @@ jobs:
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Setup macOS key chain
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup macOS key chain for app id cert
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: apple-actions/import-codesign-certs@v2
+        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}

From 09683ed7df4bc03bfd71a4baddc46f77bcb5abb7 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Fri, 3 May 2024 20:17:08 +0200
Subject: [PATCH 30/54] Remove obsolete methods (#11272)

* Remove obsolete method

* Remove obsolete CLI parameter "console"

* remove l10n

---------

Co-authored-by: Siedlerchr <siedlerkiller@gmail.com>
---
 src/main/java/org/jabref/cli/JabRefCLI.java   | 24 -------------------
 src/main/resources/l10n/JabRef_en.properties  |  1 -
 .../java/org/jabref/cli/JabRefCLITest.java    | 13 ----------
 3 files changed, 38 deletions(-)

diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
index 3d613468af5..cf78f1a2da2 100644
--- a/src/main/java/org/jabref/cli/JabRefCLI.java
+++ b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -189,9 +189,6 @@ private static Options getOptions() {
         options.addOption("v", "version", false, Localization.lang("Display version"));
         options.addOption(null, "debug", false, Localization.lang("Show debug level messages"));
 
-        // The "-console" option is handled by the install4j launcher
-        options.addOption(null, "console", false, Localization.lang("Show console output (only when the launcher is used)"));
-
         options.addOption(Option
                 .builder("i")
                 .longOpt("import")
@@ -372,25 +369,4 @@ protected static String alignStringTable(List<Pair<String, String>> table) {
 
         return sb.toString();
     }
-
-    /**
-     * Creates and wraps a multi-line and colon-seperated string from a List of Strings.
-     */
-    protected static String wrapStringList(List<String> list, int firstLineIndentation) {
-        StringBuilder builder = new StringBuilder();
-        int lastBreak = -firstLineIndentation;
-
-        for (String line : list) {
-            if (((builder.length() + 2 + line.length()) - lastBreak) > WIDTH) {
-                builder.append(",\n");
-                lastBreak = builder.length();
-                builder.append(WRAPPED_LINE_PREFIX);
-            } else if (builder.length() > 0) {
-                builder.append(", ");
-            }
-            builder.append(line);
-        }
-
-        return builder.toString();
-    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index fdb5076f8c5..b8326bbbe12 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1880,7 +1880,6 @@ Could\ not\ copy\ file=Could not copy file
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=Copied %0 files of %1 successfully to %2
 Rename\ failed=Rename failed
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef cannot access the file because it is being used by another process.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Show console output (only when the launcher is used)
 
 Remove\ line\ breaks=Remove line breaks
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Removes all line breaks in the field content.
diff --git a/src/test/java/org/jabref/cli/JabRefCLITest.java b/src/test/java/org/jabref/cli/JabRefCLITest.java
index dfcd8478cd7..8fcbbd01013 100644
--- a/src/test/java/org/jabref/cli/JabRefCLITest.java
+++ b/src/test/java/org/jabref/cli/JabRefCLITest.java
@@ -133,19 +133,6 @@ void successfulParsingOfBibtexImportLong() throws Exception {
         assertEquals(bibtex, cli.getBibtexImport());
     }
 
-    @Test
-    void wrapStringList() {
-        List<String> given = List.of("html", "simplehtml", "docbook5", "docbook4", "din1505", "bibordf", "tablerefs", "listrefs",
-                "tablerefsabsbib", "harvard", "iso690rtf", "iso690txt", "endnote", "oocsv", "ris", "misq", "yaml", "bibtexml", "oocalc", "ods",
-                "MSBib", "mods", "xmp", "pdf", "bib");
-        String expected = """
-                Available export formats: html, simplehtml, docbook5, docbook4, din1505, bibordf, tablerefs,
-                listrefs, tablerefsabsbib, harvard, iso690rtf, iso690txt, endnote, oocsv, ris, misq, yaml, bibtexml,
-                oocalc, ods, MSBib, mods, xmp, pdf, bib""";
-
-        assertEquals(expected, "Available export formats: " + JabRefCLI.wrapStringList(given, 26));
-    }
-
     @Test
     void alignStringTable() {
         List<Pair<String, String>> given = List.of(

From 505ea81daa5a033c100f2aa2fed29a145a202333 Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Mon, 6 May 2024 08:21:15 +0200
Subject: [PATCH 31/54] New Crowdin updates (#11274)

* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Spanish)

* New translations jabref_en.properties (German)

* New translations jabref_en.properties (Greek)

* New translations jabref_en.properties (Italian)

* New translations jabref_en.properties (Japanese)

* New translations jabref_en.properties (Korean)

* New translations jabref_en.properties (Dutch)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Portuguese)

* New translations jabref_en.properties (Russian)

* New translations jabref_en.properties (Swedish)

* New translations jabref_en.properties (Turkish)

* New translations jabref_en.properties (Ukrainian)

* New translations jabref_en.properties (Chinese Simplified)

* New translations jabref_en.properties (Chinese Traditional)

* New translations jabref_en.properties (Vietnamese)

* New translations jabref_en.properties (Portuguese, Brazilian)
---
 src/main/resources/l10n/JabRef_de.properties  |  9 ++---
 src/main/resources/l10n/JabRef_el.properties  |  2 --
 src/main/resources/l10n/JabRef_es.properties  |  5 ---
 src/main/resources/l10n/JabRef_fr.properties  | 16 ++++++---
 src/main/resources/l10n/JabRef_it.properties  | 16 ++++++---
 src/main/resources/l10n/JabRef_ja.properties  |  4 ---
 src/main/resources/l10n/JabRef_ko.properties  |  4 ---
 src/main/resources/l10n/JabRef_nl.properties  |  4 ---
 src/main/resources/l10n/JabRef_pl.properties  | 21 +++++++++--
 src/main/resources/l10n/JabRef_pt.properties  |  2 --
 .../resources/l10n/JabRef_pt_BR.properties    |  5 ---
 src/main/resources/l10n/JabRef_ru.properties  |  8 ++---
 src/main/resources/l10n/JabRef_sv.properties  |  2 --
 src/main/resources/l10n/JabRef_tr.properties  |  4 ---
 src/main/resources/l10n/JabRef_uk.properties  | 36 +++++++++++++++++++
 src/main/resources/l10n/JabRef_vi.properties  |  1 -
 .../resources/l10n/JabRef_zh_CN.properties    |  4 ---
 .../resources/l10n/JabRef_zh_TW.properties    |  1 -
 18 files changed, 82 insertions(+), 62 deletions(-)

diff --git a/src/main/resources/l10n/JabRef_de.properties b/src/main/resources/l10n/JabRef_de.properties
index 9d6ee1620c2..770d0680f26 100644
--- a/src/main/resources/l10n/JabRef_de.properties
+++ b/src/main/resources/l10n/JabRef_de.properties
@@ -61,7 +61,7 @@ Added\ group\ "%0".=Gruppe "%0" hinzugefügt.
 Added\ string\:\ '%0'=Zeichenkette hinzugefügt\: '%0'
 Added\ string=String hinzugefügt
 Edit\ strings=Strings bearbeiten
-Duplicate\ string\ name\:\ '%0'=Doppelter String-Name\: '%0'l
+Duplicate\ string\ name\:\ '%0'=Doppelter String-Name\: '%0'
 Modified\ string=Veränderter String
 Modified\ string\:\ '%0' =String geändert\: '%0'
 New\ string=Neuer String
@@ -276,7 +276,6 @@ Donate\ to\ JabRef=An JabRef spenden
 
 Download\ file=Datei herunterladen
 
-Downloaded\ website\ as\ an\ HTML\ file.=Webseite als HTML-Datei herunterladen.
 
 duplicate\ removal=Duplikate entfernen
 
@@ -370,7 +369,6 @@ Manage\ field\ names\ &\ content=Feldnamen & Inhalt verwalten
 Field\ to\ group\ by=Sortierfeld
 
 Filter=Filter
-Filter\ groups=Gruppen filtern
 
 Success\!\ Finished\ writing\ metadata.=Erfolgreich\! Das Schreiben der Metadaten ist abgeschlossen.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Fehler beim Schreiben von Metadaten. Details finden Sie im Fehlerprotokoll.
@@ -1878,7 +1876,6 @@ Could\ not\ copy\ file=Datei konnte nicht kopiert werden
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=Kopierte %0 Dateien von %1 erfolgreich nach %2
 Rename\ failed=Umbenennen fehlgeschlagen
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef kann nicht auf die Datei zugreifen, da sie von einem anderen Prozess verwendet wird.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Konsolenausgabe anzeigen (nur wenn der Launcher verwendet wird)
 
 Remove\ line\ breaks=Entfernen der Zeilenumbrüche
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Entfernen aller Zeilenumbrüche im Inhalt des Feldes.
@@ -2045,7 +2042,6 @@ No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=Es wurden keine LaTeX-Da
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=Der ausgewählte Eintrag hat keinen zugehörigen Zitationsschlüssel.
 Current\ search\ directory\:=Aktuelles Suchverzeichnis\:
 Set\ LaTeX\ file\ directory=LaTeX-Dateiverzeichnis festlegen
-Refresh=Aktualisieren
 Import\ entries\ from\ LaTeX\ files=Einträge aus LaTeX-Dateien importieren
 Import\ new\ entries=Neue Einträge importieren
 Group\ color=Gruppenfarbe
@@ -2157,7 +2153,7 @@ Text\ editor=Text Editor
 Search\ ShortScience=Durchsuche ShortScience
 Unable\ to\ open\ ShortScience.=Kann keine Verbindung zu ShortScience herstellen.
 
-Shared\ database=Geteilte SQL-Datenbank
+Shared\ database=Geteilte Bibliothek (SQL)
 Lookup=Nachschlagen
 
 Access\ date\ of\ the\ address\ specified\ in\ the\ url\ field.=Zugriffsdatum der im URL-Feld angegebenen Adresse.
@@ -2401,7 +2397,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=timestamp in Feld 'modi
 New\ entry\ by\ type=Neuer Eintrag nach Typ
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Datei '%1' ist ein Duplikat von '%0'. Behalte '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Datei '%1' ist ein Duplikat von '%0'. Beide werden aufgrund eines Löschfehlers beibehalten
 
 Enable\ field\ formatters=Feldformatierer aktivieren
 Entry\ Type=Eintragstyp
diff --git a/src/main/resources/l10n/JabRef_el.properties b/src/main/resources/l10n/JabRef_el.properties
index 344fc48add5..3a142fc59fb 100644
--- a/src/main/resources/l10n/JabRef_el.properties
+++ b/src/main/resources/l10n/JabRef_el.properties
@@ -261,7 +261,6 @@ Donate\ to\ JabRef=Δωρεά στο JabRef
 
 Download\ file=Κατέβασμα αρχείου
 
-Downloaded\ website\ as\ an\ HTML\ file.=Ολοκληρώθηκε η λήψη της ιστοσελίδας υπό τη μορφή HTML αρχείου.
 
 duplicate\ removal=διαγραφή διπλότυπων
 
@@ -333,7 +332,6 @@ Field\ names\ are\ not\ allowed\ to\ contain\ white\ spaces\ or\ certain\ charac
 Field\ to\ group\ by=Ομαδοποίηση με το πεδίο
 
 Filter=Φίλτρο
-Filter\ groups=Φιλτράρισμα ομάδων
 
 Success\!\ Finished\ writing\ metadata.=Επιτυχία\! Η εγγραφή των μεταδεδομένων ολοκληρώθηκε.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Σφάλμα κατά την καταγραφή μεταδεδομένων. Ανατρέξτε στο ιστορικό σφαλμάτων για λεπτομέρειες.
diff --git a/src/main/resources/l10n/JabRef_es.properties b/src/main/resources/l10n/JabRef_es.properties
index e6caaddff68..1b7b209e39b 100644
--- a/src/main/resources/l10n/JabRef_es.properties
+++ b/src/main/resources/l10n/JabRef_es.properties
@@ -273,7 +273,6 @@ Donate\ to\ JabRef=Donar a JabRef
 
 Download\ file=Descargar archivo
 
-Downloaded\ website\ as\ an\ HTML\ file.=Se descargó el sitio web como un archivo HTML.
 
 duplicate\ removal=eliminación de duplicados
 
@@ -361,7 +360,6 @@ Manage\ field\ names\ &\ content=Gestionar nombres y contenido de los campos
 Field\ to\ group\ by=Agrupar a partir de campo
 
 Filter=Filtro
-Filter\ groups=Filtros
 
 Success\!\ Finished\ writing\ metadata.=¡Éxito\! Se ha terminado de escribir metadatos.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Error al escribir los metadatos. Vea el registro de errores para más detalles.
@@ -1832,7 +1830,6 @@ Finished\ copying=Copia finalizada
 Could\ not\ copy\ file=No se puede copiar el archivo
 Rename\ failed=Error al renombrar
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef no puede acceder al archivo porque está siendo utilizado por otro proceso.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Mostrar la salida de la consola (sólo cuando se utiliza el lanzador)
 
 Remove\ line\ breaks=Eliminar saltos de línea
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Eliminar todos los saltos de línea en el contenido del campo.
@@ -1996,7 +1993,6 @@ No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=No se han encontrado arc
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=La entrada seleccionada no tiene asociada una clave de cita.
 Current\ search\ directory\:=Directorio de búsqueda actual\:
 Set\ LaTeX\ file\ directory=Establecer directorio de archivos LaTeX
-Refresh=Actualizar
 Import\ entries\ from\ LaTeX\ files=Importar entradas desde archivos LaTeX
 Import\ new\ entries=Importar nuevas entradas
 Group\ color=Color del grupo
@@ -2333,7 +2329,6 @@ Download\ operation\ canceled.=Operación de descarga cancelada.
 New\ entry\ by\ type=Entrada nueva por tipo
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=El archivo «%1» es un duplicado de «%0». Se conserva «%0»
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=El archivo «%1» es un duplicado de «%0». Se conservan ambos a causa de un error de eliminación
 
 Enable\ field\ formatters=Habilitar formateadores de campos
 Entry\ Type=Tipo de entrada
diff --git a/src/main/resources/l10n/JabRef_fr.properties b/src/main/resources/l10n/JabRef_fr.properties
index 6ad66b016ff..f08192f2c43 100644
--- a/src/main/resources/l10n/JabRef_fr.properties
+++ b/src/main/resources/l10n/JabRef_fr.properties
@@ -219,6 +219,7 @@ Custom\ entry\ types\ found\ in\ file=Types d'entrées personnalisées trouvées
 
 Customize\ entry\ types=Personnaliser les types d'entrées
 
+Customize\ keyboard\ shortcuts=Personnaliser les raccourcis clavier
 
 Cut=Couper
 
@@ -275,7 +276,6 @@ Donate\ to\ JabRef=Faire un don à JabRef
 
 Download\ file=Télécharger le fichier
 
-Downloaded\ website\ as\ an\ HTML\ file.=Site web téléchargé en tant que fichier HTML.
 
 duplicate\ removal=Suppression des doublons
 
@@ -328,6 +328,10 @@ Export\ preferences\ to\ file=Exporter les préférences vers un fichier
 Export\ to\ clipboard=Exporter vers le presse-papiers
 Export\ to\ text\ file.=Exporter vers un fichier texte.
 
+Extract\ references\ from\ file\ (online)=Extraire les références du fichier (en ligne)
+Extract\ references\ from\ file\ (offline)=Extraire les références du fichier (hors ligne)
+Extract\ References\ (online)=Extraire les références (en ligne)
+Extract\ References\ (offline)=Extraire les références (hors ligne)
 Processing\ PDF(s)=Traitement des PDF(s) en cours
 Processing\ a\ large\ number\ of\ files=Traitement d'un grand nombre de fichiers
 You\ are\ about\ to\ process\ %0\ files.\ Continue?=Vous êtes sur le point de traiter %0 fichiers. Continuer ?
@@ -365,7 +369,6 @@ Manage\ field\ names\ &\ content=Gérer les noms de champs et leur contenu
 Field\ to\ group\ by=Champ à grouper par
 
 Filter=Choix des filtres
-Filter\ groups=Filtrer les groupes
 
 Success\!\ Finished\ writing\ metadata.=Succès \! Écriture des métadonnées terminée.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Erreur lors de l'écriture des métadonnées. Consultez le journal des erreurs pour plus de détails.
@@ -506,7 +509,9 @@ Keep\ subgroups=Conserver les sous-groupes
 
 Key\ pattern=Paramétrage des clefs
 
+Keyboard\ shortcuts=Raccourcis clavier
 
+Keyboard\ shortcuts\ changed=Raccourcis clavier modifiés
 
 keys\ in\ library=clefs dans le fichier
 
@@ -1240,11 +1245,13 @@ You\ have\ to\ choose\ exactly\ two\ entries\ to\ merge.=Vous devez choisir exac
 
 Add\ timestamp\ to\ modified\ entries\ (field\ "modificationdate")=Ajouter un horodatage aux entrées modifiées (champ "modificationdate")
 Add\ timestamp\ to\ new\ entries\ (field\ "creationdate")=Ajouter un horodatage aux nouvelles entrées (champ "creationdate")
+All\ keyboard\ shortcuts\ will\ be\ reset\ to\ their\ defaults.=Tous les raccourcis clavier seront réinitialisés à leurs valeurs par défaut.
 
 Automatically\ set\ file\ links=Configurer automatiquement les liens de fichier
 Finished\ automatically\ setting\ external\ links.=La définition automatique des liens externes est terminée.
 Changed\ %0\ entries.=%0 entrées modifiées.
 
+Resetting\ all\ keyboard\ shortcuts=Réinitialisation de tous les raccourcis clavier
 
 Open\ folder=Ouvrir le répertoire
 Export\ sort\ order=Exporter l'ordre de tri
@@ -1869,7 +1876,6 @@ Could\ not\ copy\ file=Le fichier n'a pas pu être copié
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=%0 fichiers sur %1 ont été copiés avec succès vers %2
 Rename\ failed=Échec du renommage
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef ne peut pas accéder au fichier parce qu'il est utilisé par un autre processus.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Afficher la sortie de la console (uniquement nécessaire quand l'application est utilisée)
 
 Remove\ line\ breaks=Supprimer les sauts de ligne
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Supprime tous les sauts de ligne du contenu d'un champ.
@@ -2036,7 +2042,6 @@ No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=Aucun fichier LaTeX cont
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=L'entrée sélectionnée n'a pas de clef de citation associée.
 Current\ search\ directory\:=Répertoire de recherche actuel \:
 Set\ LaTeX\ file\ directory=Configurer le répertoire des fichiers LaTeX
-Refresh=Rafraîchir
 Import\ entries\ from\ LaTeX\ files=Importer des entrées à partir des fichiers LaTeX
 Import\ new\ entries=Importer de nouvelles entrées
 Group\ color=Couleur du groupe
@@ -2392,7 +2397,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Convertir le champ 'tim
 New\ entry\ by\ type=Nouvelle entrée par type
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Le fichier '%1' est un doublon de '%0'. Conservation de '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Le fichier '%1' est un doublon de '%0'. Conservation des deux en raison d'une erreur de suppression
 
 Enable\ field\ formatters=Activer les formateurs de champs
 Entry\ Type=Type d’entrée
@@ -2585,6 +2589,8 @@ Writing\ metadata\ to\ %0=Écriture des métadonnées sur %0
 
 Get\ more\ themes...=Obtenir plus de thèmes...
 
+Miscellaneous=Divers
+File-related=Lié au fichier
 
 Add\ selected\ entries\ to\ database=Ajouter les entrées sélectionnées au fichier
 The\ selected\ entry\ doesn't\ have\ a\ DOI\ linked\ to\ it.\ Lookup\ a\ DOI\ and\ try\ again.=L'entrée sélectionnée ne contient pas de DOI. Recherchez un DOI et réessayez.
diff --git a/src/main/resources/l10n/JabRef_it.properties b/src/main/resources/l10n/JabRef_it.properties
index 3a01e3b6340..5ad4fb78896 100644
--- a/src/main/resources/l10n/JabRef_it.properties
+++ b/src/main/resources/l10n/JabRef_it.properties
@@ -219,6 +219,7 @@ Custom\ entry\ types\ found\ in\ file=Tipi di voce personalizzati trovati nel fi
 
 Customize\ entry\ types=Personalizza tipi di voce
 
+Customize\ keyboard\ shortcuts=Personalizza le scorciatoie da tastiera
 
 Cut=Taglia
 
@@ -275,7 +276,6 @@ Donate\ to\ JabRef=Fai una donazione a JabRef
 
 Download\ file=Scarica il file
 
-Downloaded\ website\ as\ an\ HTML\ file.=Sito web scaricato come file HTML.
 
 duplicate\ removal=rimozione di doppioni
 
@@ -328,6 +328,10 @@ Export\ preferences\ to\ file=Esporta preferenze in un file
 Export\ to\ clipboard=Esporta negli appunti
 Export\ to\ text\ file.=Esporta su file di testo.
 
+Extract\ references\ from\ file\ (online)=Estrai i riferimenti dal file (online)
+Extract\ references\ from\ file\ (offline)=Estrai i riferimenti dal file (offline)
+Extract\ References\ (online)=Estrai Riferimenti (online)
+Extract\ References\ (offline)=Estrai i riferimenti dal file (offline)
 Processing\ PDF(s)=Elaborazione PDF
 Processing\ a\ large\ number\ of\ files=Elaborazione di un gran numero di file
 You\ are\ about\ to\ process\ %0\ files.\ Continue?=Stai per elaborare %0 file. Continuare?
@@ -365,7 +369,6 @@ Manage\ field\ names\ &\ content=Gestione nomi di campi e contenuto
 Field\ to\ group\ by=Campo di raggruppamento
 
 Filter=Filtro
-Filter\ groups=Filtra gruppi
 
 Success\!\ Finished\ writing\ metadata.=Completato con successo\! Scrivere i metadati.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Errore durante la scrittura dei metadati. Vedere il registro degli errori per i dettagli.
@@ -506,7 +509,9 @@ Keep\ subgroups=Mantieni sottogruppi
 
 Key\ pattern=Modello delle chiavi
 
+Keyboard\ shortcuts=Scorciatoie da tastiera
 
+Keyboard\ shortcuts\ changed=Scorciatoie da tastiera cambiate
 
 keys\ in\ library=Chiavi nella libreria
 
@@ -1240,11 +1245,13 @@ You\ have\ to\ choose\ exactly\ two\ entries\ to\ merge.=È necessario seleziona
 
 Add\ timestamp\ to\ modified\ entries\ (field\ "modificationdate")=Aggiungi timestamp alle voci modificate (campo "modificationdate")
 Add\ timestamp\ to\ new\ entries\ (field\ "creationdate")=Aggiungi timestamp alle nuove voci (campo "creationdate")
+All\ keyboard\ shortcuts\ will\ be\ reset\ to\ their\ defaults.=Tutte le scorciatoie da tastiera verranno reimpostate ai valori predefiniti.
 
 Automatically\ set\ file\ links=Impostazione automatica dei collegamenti ai file
 Finished\ automatically\ setting\ external\ links.=Impostazione automatica dei collegamenti esterni terminata.
 Changed\ %0\ entries.=Modificate %0 voci.
 
+Resetting\ all\ keyboard\ shortcuts=Ripristino di tutte le scorciatoie da tastiera
 
 Open\ folder=Apri cartella
 Export\ sort\ order=Esporta il modo di ordinamento
@@ -1869,7 +1876,6 @@ Could\ not\ copy\ file=Impossibile copiare il file
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=%0 file su %1 sono stati copiati correttamente in %2
 Rename\ failed=Rinomina non riuscita
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef non può accedere al file perché questo è utilizzato da un altro processo.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Mostra l'output della console (solo quando viene utilizzato il launcher)
 
 Remove\ line\ breaks=Rimuovi interruzioni di riga
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Rimuove tutte le interruzioni di riga nel contenuto del campo.
@@ -2036,7 +2042,6 @@ No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=Nessun file LaTeX conten
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=La voce selezionata non ha una chiave BibTeX associata.
 Current\ search\ directory\:=Cartella di ricerca corrente\:
 Set\ LaTeX\ file\ directory=Imposta la cartella dei file LaTeX
-Refresh=Aggiorna
 Import\ entries\ from\ LaTeX\ files=Importa le voci da file LaTeX
 Import\ new\ entries=Importa nuove voci
 Group\ color=Colore del gruppo
@@ -2392,7 +2397,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Converti il campo times
 New\ entry\ by\ type=Nuova voce per tipo
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Il file '%1' è un duplicato di '%0'. Mantenere '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Il file '%1' è un duplicato di '%0'. Mantenere entrambi a causa di errore di cancellazione
 
 Enable\ field\ formatters=Abilita formatori di campo
 Entry\ Type=Tipo di voce
@@ -2585,6 +2589,8 @@ Writing\ metadata\ to\ %0=Scrittura dei metadati su %0
 
 Get\ more\ themes...=Ottieni altri temi...
 
+Miscellaneous=Varie
+File-related=Correlato al file
 
 Add\ selected\ entries\ to\ database=Aggiungi le voci selezionate al database
 The\ selected\ entry\ doesn't\ have\ a\ DOI\ linked\ to\ it.\ Lookup\ a\ DOI\ and\ try\ again.=La voce selezionata non ha un DOI collegato ad essa. Cerca un DOI e riprova.
diff --git a/src/main/resources/l10n/JabRef_ja.properties b/src/main/resources/l10n/JabRef_ja.properties
index 8c590e3d08a..745f29b2877 100644
--- a/src/main/resources/l10n/JabRef_ja.properties
+++ b/src/main/resources/l10n/JabRef_ja.properties
@@ -263,7 +263,6 @@ Donate\ to\ JabRef=JabRefに寄付
 
 Download\ file=ファイルをダウンロード
 
-Downloaded\ website\ as\ an\ HTML\ file.=ウェブサイトを HTML ファイルとしてダウンロードしました．
 
 duplicate\ removal=重複を削除
 
@@ -342,7 +341,6 @@ Manage\ field\ names\ &\ content=フィールド名・フィールド値の管
 Field\ to\ group\ by=グループ化するフィールド
 
 Filter=フィルタ
-Filter\ groups=グループ絞り込み
 
 Success\!\ Finished\ writing\ metadata.=成功しました！メタデータの書き込みを終了しました．
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=メタデータ書き込み中にエラー．詳細についてはエラーログを参照してください．
@@ -1761,7 +1759,6 @@ Finished\ copying=コピーを終了しました
 Could\ not\ copy\ file=ファイルをコピーできませんでした
 Rename\ failed=改名に失敗しました
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=ファイルが他のプロセスによって使用されているため，JabRefがアクセスすることができません．
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=コンソール出力を表示（ロンチャーを使用する場合のみ）
 
 Remove\ line\ breaks=改行を取り除く
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=フィールドの内容から改行を全て取り除きます．
@@ -2261,7 +2258,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=timestampフィール
 New\ entry\ by\ type=型別の新規項目
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=ファイル「%1」は「%0」と重複しています．「%0」を保持します
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=ファイル「%1」は「%0」と重複しています．削除エラーが起こりましたので両方保持します
 
 Enable\ field\ formatters=フィールド整形の定義を有効にする
 Entry\ Type=項目型
diff --git a/src/main/resources/l10n/JabRef_ko.properties b/src/main/resources/l10n/JabRef_ko.properties
index a82bd22c4c7..de01984d61c 100644
--- a/src/main/resources/l10n/JabRef_ko.properties
+++ b/src/main/resources/l10n/JabRef_ko.properties
@@ -250,7 +250,6 @@ Donate\ to\ JabRef=JabRef에 기부하기
 
 Download\ file=파일 다운로드
 
-Downloaded\ website\ as\ an\ HTML\ file.=웹사이트를 HTML 파일로 다운로드했습니다.
 
 duplicate\ removal=중복 제거
 
@@ -327,7 +326,6 @@ Manage\ field\ names\ &\ content=필드 이름 및 콘텐츠 관리
 Field\ to\ group\ by=필드를 그룹화 하다
 
 Filter=필터
-Filter\ groups=그룹 필터링
 
 
 Generate=생성
@@ -1670,7 +1668,6 @@ Finished\ copying=복사 완료
 Could\ not\ copy\ file=파일을 복사할 수 없습니다
 Rename\ failed=이름 변경 실패
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef는 다른 프로세스에서 사용 중인 파일에 접근할 수 없습니다
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=콘솔 출력 표시(런처를 사용하는 경우에만)
 
 Remove\ line\ breaks=줄바꿈 제거
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=필드 내용에서 모든 줄 바꿈을 제거합니다.
@@ -2149,7 +2146,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=타임스탬프 필드
 New\ entry\ by\ type=유형별 새 항목
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=%1 파일은 %0과 동일합니다. %0을 유지합니다.
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=%1 파일은 %0과 동일합니다. \n삭제 오류로 인해 두 파일을 유지합니다.
 
 Enable\ field\ formatters=필드 포맷터 활성화
 Entry\ Type=목록 유형
diff --git a/src/main/resources/l10n/JabRef_nl.properties b/src/main/resources/l10n/JabRef_nl.properties
index 5e56cbf18e2..c9c575a3c56 100644
--- a/src/main/resources/l10n/JabRef_nl.properties
+++ b/src/main/resources/l10n/JabRef_nl.properties
@@ -267,7 +267,6 @@ Donate\ to\ JabRef=Doneer aan JabRef
 
 Download\ file=Download bestand
 
-Downloaded\ website\ as\ an\ HTML\ file.=Gedownloade website als een HTML-bestand.
 
 duplicate\ removal=duplicaten verwijderen
 
@@ -348,7 +347,6 @@ Manage\ field\ names\ &\ content=Beheer veldnamen & inhoud
 Field\ to\ group\ by=Veld te groeperen op
 
 Filter=Filteren
-Filter\ groups=Filter groepen
 
 Success\!\ Finished\ writing\ metadata.=Gelukt\! Metagegevens schrijven voltooid.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Fout tijdens het schrijven van metadata. Bekijk het foutenlogboek voor meer informatie.
@@ -1824,7 +1822,6 @@ Could\ not\ copy\ file=Kan het bestand niet kopiëren
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=%0 bestanden van %1 succesvol gekopieerd naar %2
 Rename\ failed=Hernoemen mislukt
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef kan geen toegang krijgen tot dit bestand omdat het door een ander proces wordt gebruikt.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Toon console-uitvoer (alleen wanneer de launcher wordt gebruikt)
 
 Remove\ line\ breaks=Verwijder regeleinden
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Verwijder alle regeleinden in de veldinhoud.
@@ -2332,7 +2329,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Converteer tijdsstempel
 New\ entry\ by\ type=Nieuwe invoer per type
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Bestand '%1' is een duplicaat van '%0'. Behoud '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Bestand '%1' is een duplicaat van '%0'. Beide behouden omdat de fout bij het verwijderen is
 
 Enable\ field\ formatters=Veld formatteerder inschakelen
 Entry\ Type=Invoer Type
diff --git a/src/main/resources/l10n/JabRef_pl.properties b/src/main/resources/l10n/JabRef_pl.properties
index a83d5f1fcc3..90ccfa12663 100644
--- a/src/main/resources/l10n/JabRef_pl.properties
+++ b/src/main/resources/l10n/JabRef_pl.properties
@@ -69,6 +69,7 @@ Resolve\ BibTeX\ strings=Rozwiąż ciągi znaków BibTeX
 The\ label\ of\ the\ string\ cannot\ be\ a\ number.=Etykieta ciągu znaków nie może być liczbą.
 The\ label\ of\ the\ string\ cannot\ contain\ spaces.=Etykieta ciągu znaków nie może zawierać spacji.
 The\ label\ of\ the\ string\ cannot\ contain\ the\ '\#'\ character.=Etykieta ciągu znaków nie może zawierać znaku '\#'.
+A\ string\ with\ the\ label\ '%0'\ already\ exists.=Ciąg znaków z etykietą '%0' już istnieje.
 
 All\ entries=Wszystkie wpisy
 
@@ -202,6 +203,7 @@ Custom\ entry\ types\ found\ in\ file=Znaleziono niestandardowe typy wpisów w p
 
 Customize\ entry\ types=Dostosuj typy wpisów
 
+Customize\ keyboard\ shortcuts=Dostosuj skróty klawiaturowe
 
 Cut=Wytnij
 
@@ -258,7 +260,6 @@ Donate\ to\ JabRef=Wspomóż JabRef
 
 Download\ file=Pobierz plik
 
-Downloaded\ website\ as\ an\ HTML\ file.=Pobrano stronę internetową jako plik HTML.
 
 duplicate\ removal=usuwanie duplikatów
 
@@ -311,6 +312,10 @@ Export\ preferences\ to\ file=Eksportuj ustawienia do pliku
 Export\ to\ clipboard=Eksportuj do schowka
 Export\ to\ text\ file.=Eksportuj do pliku tekstowego.
 
+Extract\ references\ from\ file\ (online)=Wyodrębnij referencje z pliku (online)
+Extract\ references\ from\ file\ (offline)=Wyodrębnij referencje z pliku (offline)
+Extract\ References\ (online)=Wyodrębnij referencje (online)
+Extract\ References\ (offline)=Wyodrębnij referencje (offline)
 Processing\ PDF(s)=Przetwarzanie PDF(ów)
 Processing\ a\ large\ number\ of\ files=Przetwarzanie dużej liczby plików
 You\ are\ about\ to\ process\ %0\ files.\ Continue?=Zamierzasz przetworzyć %0 plików. Czy chcesz kontynuować?
@@ -348,7 +353,6 @@ Manage\ field\ names\ &\ content=Zarządzaj nazwami pól i ich zawartością
 Field\ to\ group\ by=Pole do grupowania według
 
 Filter=Filtruj
-Filter\ groups=Filtruj grupy
 
 Success\!\ Finished\ writing\ metadata.=Sukces\! Zakończono zapisywanie metadanych.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Błąd podczas zapisywania metadanych. Aby uzyskać szczegółowe informacje, zobacz dziennik błędów.
@@ -366,6 +370,7 @@ Generated\ citation\ key\ for=Wygenerowano klucz cytowania dla
 Generating\ citation\ key\ for=Generowanie klucza cytowania dla
 Invalid\ citation\ key=Nieprawidłowy klucz cytowania
 
+Jump\ to\ entry\ in\ library=Przejdź do wpisu w bibliotece
 
 Autolink\ files\ with\ names\ starting\ with\ the\ citation\ key=Automatycznie podpinaj pliki z nazwami zaczynającymi się od klucza cytowania
 Autolink\ only\ files\ that\ match\ the\ citation\ key=Automatycznie podpinaj tylko pliki, które pasują do klucza cytowania
@@ -435,6 +440,7 @@ Online\ help=Pomoc online
 JabRef\ Language\ (Provides\ for\ better\ recommendations\ by\ giving\ an\ indication\ of\ user's\ preferred\ language.)=Język JabRef (zapewnia lepsze rekomendacje poprzez wskazanie preferowanego języka użytkownika).
 
 JabRef\ preferences=Preferencje JabRef
+JabRef\ Version\ (Required\ to\ ensure\ backwards\ compatibility\ with\ Mr.\ DLib's\ Web\ Service)=Wersja JabRef (wymagana do zapewnienia kompatybilności wstecznej z Mr. DLib's Web Service)
 
 Journal\ abbreviations=Skróty czasopism
 Journal\ lists\:=Listy czasopism\:
@@ -468,7 +474,9 @@ Keep\ subgroups=Zachowaj podgrupy
 
 Key\ pattern=Układ klawiszy
 
+Keyboard\ shortcuts=Skróty klawiaturowe
 
+Keyboard\ shortcuts\ changed=Zmieniono skróty klawiaturowe
 
 keys\ in\ library=klucze w bibliotece
 
@@ -768,7 +776,10 @@ Empty\ search\ ID=Pusty identyfikator wyszukiwania
 The\ given\ search\ ID\ was\ empty.=Podany identyfikator wyszukiwania był pusty.
 Clear\ search=Wyczyść wyszukiwanie
 Search\ document\ identifier\ online=Szukaj identyfikatora dokumentu online
+Search\ for\ unlinked\ local\ files=Wyszukaj niepowiązane pliki lokalne
+Search\ full\ text\ documents\ online=Wyszukaj pełne teksty dokumentów online
 Search\ term\ is\ empty.=Szukane wyrażenie jest puste.
+Invalid\ regular\ expression.=Nieprawidłowe wyrażenie regularne.
 Searching\ for\ a\ keyword=Wyszukiwanie słowa kluczowego
 
 Search\ across\ libraries\ in\ a\ new\ window=Szukaj w bibliotekach, wynik pokaż w nowym oknie
@@ -797,6 +808,7 @@ Show\ BibTeX\ source\ by\ default=Domyślnie pokaż źródło BibTeX
 
 Attached\ files=Załączone pliki
 Show\ confirmation\ dialog\ when\ deleting\ entries=Pokaż okno dialogowe potwierdzenia podczas usuwania wpisów
+Show\ confirmation\ dialog\ when\ deleting\ attached\ files=Pokaż okno dialogowe potwierdzenia podczas usuwania plików
 
 Persist\ password\ between\ sessions=Zachowaj hasło między sesjami
 
@@ -1130,9 +1142,11 @@ Parse=Parsuj
 Result=Rezultat
 You\ have\ to\ choose\ exactly\ two\ entries\ to\ merge.=Musisz wybrać dokładnie dwa wpisy do scalenia.
 
+All\ keyboard\ shortcuts\ will\ be\ reset\ to\ their\ defaults.=Wszystkie skróty klawiaturowe zostaną zresetowane do wartości domyślnych.
 
 Changed\ %0\ entries.=Zmieniono %0 wpisów.
 
+Resetting\ all\ keyboard\ shortcuts=Resetowanie wszystkich skrótów klawiaturowych
 
 Open\ folder=Otwórz folder
 Export\ sort\ order=Eksportuj kolejność sortowania
@@ -1578,7 +1592,6 @@ files=pliki
 
 No\ citations\ found=Nie znaleziono cytatów
 Current\ search\ directory\:=Aktualny katalog wyszukiwania\:
-Refresh=Odśwież
 Import\ entries\ from\ LaTeX\ files=Importuj wpisy z plików LaTeX
 Import\ new\ entries=Importuj nowe wpisy
 
@@ -1744,6 +1757,8 @@ Finished\ writing\ metadata\ for\ library\ %0\ (%1\ succeeded,\ %2\ skipped,\ %3
 Processing...=Przetwarzanie...
 
 
+Miscellaneous=Pozostałe
+File-related=Związane z plikami
 
 Cancel\ search=Anuluj wyszukiwanie
 Select\ entry=Wybierz wpis
diff --git a/src/main/resources/l10n/JabRef_pt.properties b/src/main/resources/l10n/JabRef_pt.properties
index 03189da0ac7..6a496f87516 100644
--- a/src/main/resources/l10n/JabRef_pt.properties
+++ b/src/main/resources/l10n/JabRef_pt.properties
@@ -261,7 +261,6 @@ Donate\ to\ JabRef=Doar para JabRef
 
 Download\ file=Download do arquivo
 
-Downloaded\ website\ as\ an\ HTML\ file.=Site baixado como arquivo HTML.
 
 duplicate\ removal=remoção de duplicatas
 
@@ -338,7 +337,6 @@ Manage\ field\ names\ &\ content=Gerenciar nomes e conteúdo dos campos
 Field\ to\ group\ by=Campos como critério de agrupamento
 
 Filter=Filtro
-Filter\ groups=Filtrar grupos
 
 Success\!\ Finished\ writing\ metadata.=Sucesso\! Escrita de metadados finalizada.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Erro ao escrever metadados. Consulte o log de erros para obter detalhes.
diff --git a/src/main/resources/l10n/JabRef_pt_BR.properties b/src/main/resources/l10n/JabRef_pt_BR.properties
index 94fed9e733e..7f7fdc2cfaf 100644
--- a/src/main/resources/l10n/JabRef_pt_BR.properties
+++ b/src/main/resources/l10n/JabRef_pt_BR.properties
@@ -271,7 +271,6 @@ Donate\ to\ JabRef=Doar para JabRef
 
 Download\ file=Download do arquivo
 
-Downloaded\ website\ as\ an\ HTML\ file.=Site baixado como arquivo HTML.
 
 duplicate\ removal=remoção de duplicatas
 
@@ -361,7 +360,6 @@ Manage\ field\ names\ &\ content=Gerenciar nomes e conteúdo dos campos
 Field\ to\ group\ by=Campos como critério de agrupamento
 
 Filter=Filtro
-Filter\ groups=Filtrar grupos
 
 Success\!\ Finished\ writing\ metadata.=Sucesso\! Terminou a escrita de metadados.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Erro ao escrever metadados. Consulte o log de erros para obter detalhes.
@@ -1864,7 +1862,6 @@ Could\ not\ copy\ file=Não foi possível copiar o arquivo
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=%0 arquivos de %1 copiados com sucesso para %2
 Rename\ failed=Falha ao renomear
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef não pode acessar o arquivo porque ele está sendo usado por outro processo.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Mostrar saída do console (somente quando o launcher é usado)
 
 Remove\ line\ breaks=Remover quebras de linha
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Remove todas as quebras de linha do conteúdo do campo.
@@ -2031,7 +2028,6 @@ No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=Nenhum arquivo LaTeX con
 Selected\ entry\ does\ not\ have\ an\ associated\ citation\ key.=O item selecionado não tem uma chave de citação associada.
 Current\ search\ directory\:=Diretório de pesquisa atual\:
 Set\ LaTeX\ file\ directory=Definir diretório de arquivos LaTeX
-Refresh=Atualizar
 Import\ entries\ from\ LaTeX\ files=Importar referências a partir dos arquivos LaTeX
 Import\ new\ entries=Importar novas referências
 Group\ color=Cor do grupo
@@ -2387,7 +2383,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Converter campo timesta
 New\ entry\ by\ type=Nova entrada por tipo
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Arquivo '%1' é uma duplicata de '%0'. Mantendo '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Arquivo '%1' é uma duplicata de '%0'. Mantendo ambos devido a um erro de exclusão
 
 Enable\ field\ formatters=Ativar formatadores de campo
 Entry\ Type=Tipo de referência
diff --git a/src/main/resources/l10n/JabRef_ru.properties b/src/main/resources/l10n/JabRef_ru.properties
index 1b92c78994a..bfbf49c6868 100644
--- a/src/main/resources/l10n/JabRef_ru.properties
+++ b/src/main/resources/l10n/JabRef_ru.properties
@@ -255,7 +255,6 @@ Donate\ to\ JabRef=Поддержать JabRef
 
 Download\ file=Загрузить файл
 
-Downloaded\ website\ as\ an\ HTML\ file.=Загружен сайт в формате HTML.
 
 duplicate\ removal=удаление дубликатов
 
@@ -334,7 +333,6 @@ Manage\ field\ names\ &\ content=Управлять названиями пол
 Field\ to\ group\ by=Поле для группировки
 
 Filter=Фильтр
-Filter\ groups=Фильтровать группы
 
 Success\!\ Finished\ writing\ metadata.=Успех\! Запись метаданных завершена.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Ошибка при записи метаданных. Смотрите журнал ошибок для подробностей.
@@ -442,6 +440,10 @@ Journal\ abbreviations=Сокращения для журналов
 Journal\ lists\:=Список журналов\:
 Remove\ journal\ '%0'=Удалить журнал '%0'
 
+Year=Год
+Categories=Категории
+ISSN=ISSN
+Publisher=Издатель
 
 
 Keep\ both=Оставить оба
@@ -1729,7 +1731,6 @@ Finished\ copying=Копирование завершено
 Could\ not\ copy\ file=Невозможно скопировать файл
 Rename\ failed=Не удалось переименовать
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef не может получить доступ к файлу, так как он используется другим процессом.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Показывать вывод консоли (только при использовании лаунчера)
 
 Remove\ line\ breaks=Удалить разрывы строк
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Удаляет все разрывы строк в содержимом поля.
@@ -2226,7 +2227,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Преобразова
 New\ entry\ by\ type=Новая запись по типу
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=Файл '%1' является дубликатом '%0'. Оставлен '%0'
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=Файл '%1' является дубликатом '%0'. Оставлены оба из-за ошибки удаления
 
 Enable\ field\ formatters=Включить форматирование полей
 Entry\ Type=Тип записи
diff --git a/src/main/resources/l10n/JabRef_sv.properties b/src/main/resources/l10n/JabRef_sv.properties
index 569743a1f1c..e4ba746185c 100644
--- a/src/main/resources/l10n/JabRef_sv.properties
+++ b/src/main/resources/l10n/JabRef_sv.properties
@@ -249,7 +249,6 @@ Donate\ to\ JabRef=Donera till JabRef
 
 Download\ file=Ladda ned fil
 
-Downloaded\ website\ as\ an\ HTML\ file.=Webbsida nedladdad som html-fil.
 
 duplicate\ removal=ta bort dubbletter
 
@@ -328,7 +327,6 @@ Manage\ field\ names\ &\ content=Hantera fältnamn & innehåll
 Field\ to\ group\ by=Fält att använda för gruppering
 
 Filter=Filtrera
-Filter\ groups=Filtrera grupper
 
 
 Generate=Generera
diff --git a/src/main/resources/l10n/JabRef_tr.properties b/src/main/resources/l10n/JabRef_tr.properties
index abb65c2f6ae..bfac7f74ea2 100644
--- a/src/main/resources/l10n/JabRef_tr.properties
+++ b/src/main/resources/l10n/JabRef_tr.properties
@@ -269,7 +269,6 @@ Donate\ to\ JabRef=JabRef'e bağış yap
 
 Download\ file=Dosya indir
 
-Downloaded\ website\ as\ an\ HTML\ file.=Web sitesi bir HTML dosyası olarak indirildi.
 
 duplicate\ removal=çift nüsha silme
 
@@ -356,7 +355,6 @@ Manage\ field\ names\ &\ content=Alan ad ve içeriklerini yönet
 Field\ to\ group\ by=Gruplanacak alan
 
 Filter=Süzgeç
-Filter\ groups=Grupları filtrele
 
 Success\!\ Finished\ writing\ metadata.=Başarılı\! Metaverisi yazma bitirildi.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=Metaverisi yazılırken hata. Ayrıntılar için hata kayıtlarına bakın.
@@ -1843,7 +1841,6 @@ Could\ not\ copy\ file=Dosya kopyalanamadı
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=%1 dosyanın %0'i başarıyla %2'e kopyalandı
 Rename\ failed=Yeniden adlandırma başarısız oldu
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef dosyaya erişemiyor çünkü dosya başka bir süreç tarafından kullanılıyor.
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Konsol çıktısını göster (yalnızca başlatıcı kullanıldığında)
 
 Remove\ line\ breaks=Satır sonlarını kaldır
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=Alan içeriğindeki tüm satır sonlarını kaldırır.
@@ -2363,7 +2360,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=Tarih bilgisi alanını
 New\ entry\ by\ type=Türle yeni girdi
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'='%1' dosyası '%0'ın tıpkısı. '%0' tutuluyor
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error='%1' dosyası '%0'ın tıpkısı. Silme hatası nedeniyle ikisi de tutuluyor
 
 Enable\ field\ formatters=Alan biçimlendiricilerini etkinleştir
 Entry\ Type=Girdi Türü
diff --git a/src/main/resources/l10n/JabRef_uk.properties b/src/main/resources/l10n/JabRef_uk.properties
index 5ccd342ef5d..b39e7976f6b 100644
--- a/src/main/resources/l10n/JabRef_uk.properties
+++ b/src/main/resources/l10n/JabRef_uk.properties
@@ -60,6 +60,7 @@ Added\ group\ "%0".=Додана група
 
 Added\ string\:\ '%0'=Додано рядок
 Added\ string=Додано рядок
+Must\ not\ be\ empty\!=Не може бути порожнім\!
 
 All\ entries=Всі записи
 
@@ -90,12 +91,20 @@ Application\ to\ push\ entries\ to=Заявка на push матеріалів
 
 
 
+Cancel=Скасувати
+Cannot\ create\ group=Не вдається створити групу
 
+Cannot\ create\ group.\ Please\ create\ a\ library\ first.=Не вдається створити групу. Будь ласка, спочатку створіть бібліотеку.
 
+Cannot\ open\ folder\ as\ the\ file\ is\ an\ online\ link.=Не вдається відкрити папку, оскільки файл є посиланням.
 
+case\ insensitive=без урахування регістру
 
+case\ sensitive=з урахуванням регістру
 
+Case\ sensitive=З урахуванням регістру
 
+change\ assignment\ of\ entries=змінити призначення записів
 
 
 
@@ -107,24 +116,51 @@ Application\ to\ push\ entries\ to=Заявка на push матеріалів
 
 
 
+Open\ /\ close\ entry\ editor=Відкрити / закрити редактор записів
 
+Close\ dialog=Закрити діалог
 
+Close\ the\ current\ library=Закрити поточну бібліотеку
 
+Close\ window=Закрити вікно
 
+Comments=Коментарі
 
+Contained\ in=Міститься в
 
+Content=Зміст
 
+Copy=Копіювати
 
+Copy\ title=Копіювати заголовок
+Copy\ citation\ (html)=Копіювати цитування (html)
+Copy\ citation\ (text)=Копіювати цитування (текст)
+Copy\ citation\ key=Копіювати ключ цитування
+Copy\ citation\ key\ and\ link=Копіювати ключ цитування та посилання
+Copy\ citation\ key\ and\ title=Копіювати ключ цитування та заголовок
+Copy\ citation\ key\ with\ configured\ cite\ command=Копіювати ключ цитування з налаштованою командою цитування
 
+Copy\ to\ clipboard=Копіювати в буфер обміну
 
+Could\ not\ call\ executable=Не вдалося викликати виконавчий файл
 
+Could\ not\ export\ preferences=Не вдалося експортувати налаштування
 
+Could\ not\ find\ a\ suitable\ import\ format.=Не вдалося знайти відповідний формат імпорту.
+Could\ not\ import\ preferences=Не вдалося імпортувати налаштування
 
+Could\ not\ instantiate\ %0=Не вдалося створити %0
+Could\ not\ instantiate\ %0\ %1=Не вдалося створити %0 %1
+Could\ not\ instantiate\ %0.\ Have\ you\ chosen\ the\ correct\ package\ path?=Не вдалося створити %0. Ви обрали правильний шлях до пакету?
 
+Could\ not\ print\ preview=Не вдалося надрукувати попередній перегляд
 
+Create\ custom\ fields\ for\ each\ BibTeX\ entry=Створити власні поля для кожного запису BibTeX
 
 
+Current\ content\:\ %0=Поточний вміст\: %0
 
+Current\ value\:\ %0=Поточне значення\: %0
 
 
 
diff --git a/src/main/resources/l10n/JabRef_vi.properties b/src/main/resources/l10n/JabRef_vi.properties
index 49979058375..7187fdcf00f 100644
--- a/src/main/resources/l10n/JabRef_vi.properties
+++ b/src/main/resources/l10n/JabRef_vi.properties
@@ -284,7 +284,6 @@ Field\ name=Tên dữ liệu
 Field\ to\ group\ by=Dữ liệu gộp nhóm theo
 
 Filter=Lọc
-Filter\ groups=Nhóm bộ lọc
 
 
 Generate=Tạo
diff --git a/src/main/resources/l10n/JabRef_zh_CN.properties b/src/main/resources/l10n/JabRef_zh_CN.properties
index 6bd3ae6c20f..f2276cf4d21 100644
--- a/src/main/resources/l10n/JabRef_zh_CN.properties
+++ b/src/main/resources/l10n/JabRef_zh_CN.properties
@@ -267,7 +267,6 @@ Donate\ to\ JabRef=Donate
 
 Download\ file=下载文件
 
-Downloaded\ website\ as\ an\ HTML\ file.=将网站下载为HTML文件。
 
 duplicate\ removal=移除重复
 
@@ -348,7 +347,6 @@ Manage\ field\ names\ &\ content=管理字段名称和内容
 Field\ to\ group\ by=用来分组的字段
 
 Filter=筛选
-Filter\ groups=筛选组
 
 Success\!\ Finished\ writing\ metadata.=Success\! Finished writing metadata.
 Error\ while\ writing\ metadata.\ See\ the\ error\ log\ for\ details.=写入元数据时出错。详细信息请参阅错误日志。
@@ -1812,7 +1810,6 @@ Could\ not\ copy\ file=无法复制文件
 Copied\ %0\ files\ of\ %1\ successfully\ to\ %2=Copied %0 files of %1 successfully to %2
 Rename\ failed=重命名失败
 JabRef\ cannot\ access\ the\ file\ because\ it\ is\ being\ used\ by\ another\ process.=JabRef 无法访问该文件, 因为另一个进程正在使用它。
-Show\ console\ output\ (only\ when\ the\ launcher\ is\ used)=Show console output (only when the launcher is used)
 
 Remove\ line\ breaks=移除换行符
 Removes\ all\ line\ breaks\ in\ the\ field\ content.=移除字段内容中的所有换行符。
@@ -2320,7 +2317,6 @@ Convert\ timestamp\ field\ to\ field\ 'modificationdate'=将 timestamp 字段转
 New\ entry\ by\ type=按类型创建新条目
 
 File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ '%0'=文件%1是%0的重复。保留%0
-File\ '%1'\ is\ a\ duplicate\ of\ '%0'.\ Keeping\ both\ due\ to\ deletion\ error=文件%1是%0的重复。由于删除错误同时保留两者。
 
 Enable\ field\ formatters=启用字段格式化器
 Entry\ Type=条目类型
diff --git a/src/main/resources/l10n/JabRef_zh_TW.properties b/src/main/resources/l10n/JabRef_zh_TW.properties
index e75a7a1d852..050baf57ba6 100644
--- a/src/main/resources/l10n/JabRef_zh_TW.properties
+++ b/src/main/resources/l10n/JabRef_zh_TW.properties
@@ -280,7 +280,6 @@ Field\ names\ are\ not\ allowed\ to\ contain\ white\ spaces\ or\ certain\ charac
 
 
 Filter=篩選
-Filter\ groups=篩選群組
 
 
 Generate=生成

From 3f88e6e9c7f6456bfeaa2cad4555d612fe0ac35f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:34:08 +0000
Subject: [PATCH 32/54] Bump org.apache.commons:commons-text from 1.11.0 to
 1.12.0 (#11275)

Bumps org.apache.commons:commons-text from 1.11.0 to 1.12.0.

---
updated-dependencies:
- dependency-name: org.apache.commons:commons-text
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 11ed7431454..9be7e392f5f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -164,7 +164,7 @@ dependencies {
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
-    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.11.0'
+    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
     implementation 'com.h2database:h2-mvstore:2.2.224'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635

From c2888d844bf1b474bffd5c0bc8769101753669cb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:34:15 +0000
Subject: [PATCH 33/54] Bump jakarta.ws.rs:jakarta.ws.rs-api from 3.1.0 to
 4.0.0 (#11276)

Bumps jakarta.ws.rs:jakarta.ws.rs-api from 3.1.0 to 4.0.0.

---
updated-dependencies:
- dependency-name: jakarta.ws.rs:jakarta.ws.rs-api
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9be7e392f5f..8137ad0b950 100644
--- a/build.gradle
+++ b/build.gradle
@@ -268,7 +268,7 @@ dependencies {
     implementation group: 'org.jooq', name: 'jool', version: '0.9.15'
     // JAX-RS implemented by Jersey
     // API
-    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.1.0'
+    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:4.0.0'
     // Implementation of the API
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.6'
     // injection framework

From a9983a0573a2d7a3d1c512f352db37fd1221ee4a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:34:35 +0000
Subject: [PATCH 34/54] Bump org.apache.commons:commons-csv from 1.10.0 to
 1.11.0 (#11277)

Bumps [org.apache.commons:commons-csv](https://github.com/apache/commons-csv) from 1.10.0 to 1.11.0.
- [Changelog](https://github.com/apache/commons-csv/blob/master/RELEASE-NOTES.txt)
- [Commits](https://github.com/apache/commons-csv/compare/rel/commons-csv-1.10.0...rel/commons-csv-1.11.0)

---
updated-dependencies:
- dependency-name: org.apache.commons:commons-csv
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8137ad0b950..c03acc2782a 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     implementation "org.apache.lucene:lucene-analysis-common:$luceneVersion"
     implementation "org.apache.lucene:lucene-highlighter:$luceneVersion"
 
-    implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
+    implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.11.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
     implementation 'com.h2database:h2-mvstore:2.2.224'

From 17ba16307a26586399d6d892293f2f366aafedd7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:37:52 +0000
Subject: [PATCH 35/54] Bump com.dlsc.gemsfx:gemsfx from 2.10.0 to 2.12.0
 (#11278)

Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.10.0 to 2.12.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/jreleaser.yml)
- [Commits](https://github.com/dlsc-software-consulting-gmbh/GemsFX/compare/v2.10.0...v2.12.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index c03acc2782a..e001f630b52 100644
--- a/build.gradle
+++ b/build.gradle
@@ -218,7 +218,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.10.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.12.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.openjfx'

From 35089520d7f014268b85a854f68102c46064179b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:41:06 +0000
Subject: [PATCH 36/54] Bump io.github.classgraph:classgraph from 4.8.170 to
 4.8.172 (#11279)

Bumps [io.github.classgraph:classgraph](https://github.com/classgraph/classgraph) from 4.8.170 to 4.8.172.
- [Release notes](https://github.com/classgraph/classgraph/releases)
- [Commits](https://github.com/classgraph/classgraph/compare/classgraph-4.8.170...classgraph-4.8.172)

---
updated-dependencies:
- dependency-name: io.github.classgraph:classgraph
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index e001f630b52..b3190ce21e2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -298,7 +298,7 @@ dependencies {
 
     implementation 'commons-io:commons-io:2.16.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.170'
+    testImplementation 'io.github.classgraph:classgraph:4.8.172'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 

From f346a448519c8a8a45d211cd24ea026e8756545c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 6 May 2024 14:57:19 +0000
Subject: [PATCH 37/54] Bump src/main/resources/csl-styles from `32348cb` to
 `5338902` (#11280)

Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `32348cb` to `5338902`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](https://github.com/citation-style-language/styles/compare/32348cb790b809081a0ff42ce81f6bcba050e4de...533890226e8abbbeb31cd63a5b1180ffc6e4870d)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-styles
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 src/main/resources/csl-styles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
index 32348cb790b..533890226e8 160000
--- a/src/main/resources/csl-styles
+++ b/src/main/resources/csl-styles
@@ -1 +1 @@
-Subproject commit 32348cb790b809081a0ff42ce81f6bcba050e4de
+Subproject commit 533890226e8abbbeb31cd63a5b1180ffc6e4870d

From 858168922c8be2346fa5e1a79e0396d0983139ff Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Tue, 7 May 2024 02:24:42 +0200
Subject: [PATCH 38/54] Fix missing add opens for javafx on mac (#11273)

* Fix missing add opens for javafx on mac

fixes https://github.com/JabRef/jabref-issue-melting-pot/issues/428

* add also to org.jabref
---
 .github/workflows/deployment-arm64.yml | 17 +++++++++++++++--
 .github/workflows/deployment.yml       | 18 ++++++++++++++++--
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
index 01675246e2b..a7337738223 100644
--- a/.github/workflows/deployment-arm64.yml
+++ b/.github/workflows/deployment-arm64.yml
@@ -130,7 +130,14 @@ jobs:
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref.merged.module \
-          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module
+          --java-options --add-opens=javafx.controls/javafx.scene.control.skin=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref \
+          --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
       - name: Build pkg (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
@@ -160,7 +167,13 @@ jobs:
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref.merged.module \
-          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref \
+          --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
       - name: Rename files with arm64 suffix as well
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index 0fe694d2a30..030790397d1 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -142,7 +142,14 @@ jobs:
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref.merged.module \
-          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module
+          --java-options --add-opens=javafx.controls/javafx.scene.control.skin=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref \
+          --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
       - name: Build pkg (macOS)
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
@@ -172,7 +179,14 @@ jobs:
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref.merged.module \
-          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module
+          --java-options --add-opens=javafx.controls/javafx.scene.control.skin=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref \
+          --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
+          --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
       - name: Build runtime image and installer (linux, Windows)
         if: (matrix.os != 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash

From 045f8157a2916fe8b7b004ca67ae215cf0c106f0 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 7 May 2024 23:51:33 +0200
Subject: [PATCH 39/54] Fix jacoco plugin (#11283)

---
 build.gradle                | 16 +++---
 docs/code-howtos/testing.md | 97 +++++++++++++++++++++++--------------
 2 files changed, 70 insertions(+), 43 deletions(-)

diff --git a/build.gradle b/build.gradle
index b3190ce21e2..6466119ed31 100644
--- a/build.gradle
+++ b/build.gradle
@@ -575,16 +575,18 @@ databaseTest.mustRunAfter jacocoPrepare
 fetcherTest.mustRunAfter jacocoPrepare
 
 jacocoTestReport {
+    dependsOn jacocoPrepare, test, fetcherTest, databaseTest
+
     executionData files(
-            "$buildDir/jacoco/test.exec",
-            "$buildDir/jacoco/databaseTest.exec",
-            "$buildDir/jacoco/fetcherTest.exec").filter { it.exists() }
-    dependsOn jacocoPrepare, test, databaseTest, fetcherTest
+            layout.buildDirectory.file('jacoco/test.exec').get().asFile,
+            layout.buildDirectory.file('jacoco/fetcherTest.exec').get().asFile,
+            layout.buildDirectory.file('jacoco/databaseTest.exec').get().asFile)
 
     reports {
-        csv.getRequired().set(true)
-        html.getRequired().set(true)
-        xml.getRequired().set(true) // coveralls plugin depends on xml format report
+        csv.required = true
+        html.required = true
+        // coveralls plugin depends on xml format report
+        xml.required = true
     }
 }
 
diff --git a/docs/code-howtos/testing.md b/docs/code-howtos/testing.md
index 88a9f6d3dbc..88f8ab84d12 100644
--- a/docs/code-howtos/testing.md
+++ b/docs/code-howtos/testing.md
@@ -3,20 +3,7 @@ parent: Code Howtos
 ---
 # Testing JabRef
 
-## Background on Java testing
-
-In JabRef, we mainly rely on basic JUnit tests to increase code coverage. There are other ways to test:
-
-| Type           | Techniques                                 | Tool (Java)                                                             | Kind of tests                                                  | Used In JabRef                                                |
-| -------------- | ------------------------------------------ | ----------------------------------------------------------------------- | -------------------------------------------------------------- | ------------------------------------------------------------- |
-| Functional     | Dynamics, black box, positive and negative | [JUnit-QuickCheck](https://github.com/pholser/junit-quickcheck)         | Random data generation                                         | No, not intended, because other test kinds seem more helpful. |
-| Functional     | Dynamics, black box, positive and negative | [GraphWalker](https://graphwalker.github.io)                            | Model-based                                                    | No, because the BibDatabase doesn't need to be tests          |
-| Functional     | Dynamics, black box, positive and negative | [TestFX](https://github.com/TestFX/TestFX)                              | GUI Tests                                                      | Yes                                                           |
-| Functional     | Dynamics, white box, negative              | [PIT](https://pitest.org)                                               | Mutation                                                       | No                                                            |
-| Functional     | Dynamics, white box, positive and negative | [Mockito](https://site.mockito.org)                                     | Mocking                                                        | Yes                                                           |
-| Non-functional | Dynamics, black box, positive and negative | [JETM](http://jetm.void.fm), [Apache JMeter](https://jmeter.apache.org) | Performance (performance testing vs load testing respectively) | No                                                            |
-| Structural     | Static, white box                          | [CheckStyle](https://checkstyle.sourceforge.io)                         | Constient formatting of the source code                        | Yes                                                           |
-| Structural     | Dynamics, white box                        | [SpotBugs](https://spotbugs.github.io)                                  | Reocurreing bugs (based on experience of other projects)       | No                                                            |
+In JabRef, we mainly rely on basic [JUnit](https://junit.org/junit5/docs/current/user-guide/) unit tests to increase code coverage.
 
 ## General hints on tests
 
@@ -27,10 +14,10 @@ Imagine you want to test the method `format(String value)` in the class `BracesF
 * _Test only one thing per test:_ tests should be short and test only one small part of the method. So instead of
 
     ```java
-    testFormat() {
-     assertEqual("test", format("test"));
-     assertEqual("{test", format("{test"));
-     assertEqual("test", format("test}}"));
+    void format() {
+        assertEqual("test", format("test"));
+        assertEqual("{test", format("{test"));
+        assertEqual("test", format("test}}"));
     }
     ```
 
@@ -38,18 +25,42 @@ Imagine you want to test the method `format(String value)` in the class `BracesF
 * Do _not just test happy paths_, but also wrong/weird input.
 * It is recommended to write tests _before_ you actually implement the functionality (test driven development).
 * _Bug fixing:_ write a test case covering the bug and then fix it, leaving the test as a security that the bug will never reappear.
-* Do not catch exceptions in tests, instead use the `assertThrows(Exception.class, ()->doSomethingThrowsEx())` feature of [junit-jupiter](https://junit.org/junit5/docs/current/user-guide/) to the test method.
+* Do not catch exceptions in tests, instead use the `assertThrows(Exception.class, () -> doSomethingThrowsEx())` feature of [junit-jupiter](https://junit.org/junit5/docs/current/user-guide/) to the test method.
+
+## Coverage
+
+IntelliJ has build in test coverage reports. Choose "Run with coverage".
+
+For a full coverage report as HTML, execute the gradle task `jacocoTestReport` (available in the "verification" folder in IntelliJ).
+Then, you will find <build/reports/jacoco/test/html/index.html> which shows the coverage of the tests.
 
 ## Lists in tests
 
-* Use `assertEquals(Collections.emptyList(), actualList);` instead of `assertEquals(0, actualList.size());` to test whether a list is empty.
-* Similarly, use `assertEquals(Arrays.asList("a", "b"), actualList);` to compare lists instead of
+Instead of
 
-    ```java
-           assertEquals(2, actualList.size());
-           assertEquals("a", actualList.get(0));
-           assertEquals("b", actualList.get(1));
-    ```
+```java
+assertTrue(actualList.isEmpty());
+```
+
+use
+
+```java
+assertEquals(List.of(), actualList);
+```
+
+Similarly, to compare lists, instead of following code:
+
+```java
+assertEquals(2, actualList.size());
+assertEquals("a", actualList.get(0));
+assertEquals("b", actualList.get(1));
+```
+
+use the following code:
+
+```java
+assertEquals(List.of("a", "b"), actualList);
+```
 
 ## BibEntries in tests
 
@@ -57,19 +68,18 @@ Imagine you want to test the method `format(String value)` in the class `BracesF
 
 ## Files and folders in tests
 
-* If you need a temporary file in tests, then add the following Annotation before the class:
+If you need a temporary file in tests, use the `@TempDir` annotation:
 
-    ```java
-    @ExtendWith(TempDirectory.class)
-    class TestClass{
+```java
+class TestClass{
 
-      @BeforeEach
-      void setUp(@TempDirectory.TempDir Path temporaryFolder){
-      }
-    }
-    ```
+  @Test
+  void deletionWorks(@TempDir Path tempDir) {
+  }
+}
+```
 
-    to the test class. A temporary file is now created by `Files.createFile(path)`. Using this pattern automatically ensures that the test folder is deleted after the tests are run. See the [junit-pioneer doc](https://junit-pioneer.org/docs/temp-directory/) for more details.
+to the test class. A temporary file is now created by `Files.createFile(path)`. Using this pattern automatically ensures that the test folder is deleted after the tests are run. See <https://www.geeksforgeeks.org/junit-5-tempdir/>  for more details.
 
 ## Loading Files from Resources
 
@@ -129,3 +139,18 @@ docker run -e MYSQL_ROOT_PASSWORD=root -e MYSQL_DATABASE=jabref -p 3800:3307 mys
 ```
 
 Set the environment variable `DBMS` to `mysql`.
+
+## Advanced testing and further reading
+
+On top of basic unit testing, there are more ways to test a software:
+
+| Type           | Techniques                                 | Tool (Java)                                                             | Kind of tests                                                  | Used In JabRef                                                |
+| -------------- | ------------------------------------------ | ----------------------------------------------------------------------- | -------------------------------------------------------------- | ------------------------------------------------------------- |
+| Functional     | Dynamics, black box, positive and negative | [JUnit-QuickCheck](https://github.com/pholser/junit-quickcheck)         | Random data generation                                         | No, not intended, because other test kinds seem more helpful. |
+| Functional     | Dynamics, black box, positive and negative | [GraphWalker](https://graphwalker.github.io)                            | Model-based                                                    | No, because the BibDatabase doesn't need to be tests          |
+| Functional     | Dynamics, black box, positive and negative | [TestFX](https://github.com/TestFX/TestFX)                              | GUI Tests                                                      | Yes                                                           |
+| Functional     | Dynamics, white box, negative              | [PIT](https://pitest.org)                                               | Mutation                                                       | No                                                            |
+| Functional     | Dynamics, white box, positive and negative | [Mockito](https://site.mockito.org)                                     | Mocking                                                        | Yes                                                           |
+| Non-functional | Dynamics, black box, positive and negative | [JETM](http://jetm.void.fm), [Apache JMeter](https://jmeter.apache.org) | Performance (performance testing vs load testing respectively) | No                                                            |
+| Structural     | Static, white box                          | [CheckStyle](https://checkstyle.sourceforge.io)                         | Constient formatting of the source code                        | Yes                                                           |
+| Structural     | Dynamics, white box                        | [SpotBugs](https://spotbugs.github.io)                                  | Reocurreing bugs (based on experience of other projects)       | No                                                            |

From fb93c2f5958eac92c41ea3d64fe5b377a55ba0e6 Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Wed, 8 May 2024 22:36:20 +0200
Subject: [PATCH 40/54] Store preview divider pos in entry editor (#11285)

* Store preview divider pos in entry editor


Fixes https://github.com/JabRef/jabref/issues/11281

* checkstyle
---
 CHANGELOG.md                                  |  1 +
 .../entryeditor/EntryEditorPreferences.java   | 20 ++++++++++++++++++-
 .../gui/entryeditor/FieldsEditorTab.java      | 15 ++++++++++++++
 .../jabref/preferences/JabRefPreferences.java | 10 ++++++++--
 4 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 410b5341a73..b972f15d2cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where drag and dropping entries created a shallow copy. [#11160](https://github.com/JabRef/jabref/issues/11160)
 - We fixed an issue where imports to a custom group would only work for the first entry [#11085](https://github.com/JabRef/jabref/issues/11085), [#11269](https://github.com/JabRef/jabref/issues/11269)
 - We fixed an issue where a new entry was not added to the selected group [#8933](https://github.com/JabRef/jabref/issues/8933)
+- We fixed an issue where the horizontal position of the Entry Preview inside the entry editor was not remembered across restarts [#11281](https://github.com/JabRef/jabref/issues/11281)
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java
index ae0fda0194c..fcca2b100ad 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java
@@ -49,6 +49,7 @@ public static JournalPopupEnabled fromString(String status) {
     private final ObjectProperty<JournalPopupEnabled> enablementStatus;
     private final BooleanProperty shouldShowSciteTab;
     private final BooleanProperty showUserCommentsFields;
+    private final DoubleProperty previewWidthDividerPosition;
 
     public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
                                   Map<String, Set<Field>> defaultEntryEditorTabList,
@@ -62,7 +63,8 @@ public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
                                   boolean autolinkFilesEnabled,
                                   JournalPopupEnabled journalPopupEnabled,
                                   boolean showSciteTab,
-                                  boolean showUserCommentsFields) {
+                                  boolean showUserCommentsFields,
+                                  double previewWidthDividerPosition) {
 
         this.entryEditorTabList = new SimpleMapProperty<>(FXCollections.observableMap(entryEditorTabList));
         this.defaultEntryEditorTabList = new SimpleMapProperty<>(FXCollections.observableMap(defaultEntryEditorTabList));
@@ -77,6 +79,7 @@ public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
         this.enablementStatus = new SimpleObjectProperty<>(journalPopupEnabled);
         this.shouldShowSciteTab = new SimpleBooleanProperty(showSciteTab);
         this.showUserCommentsFields = new SimpleBooleanProperty(showUserCommentsFields);
+        this.previewWidthDividerPosition = new SimpleDoubleProperty(previewWidthDividerPosition);
     }
 
     public ObservableMap<String, Set<Field>> getEntryEditorTabs() {
@@ -226,4 +229,19 @@ public BooleanProperty showUserCommentsFieldsProperty() {
     public void setShowUserCommentsFields(boolean showUserCommentsFields) {
         this.showUserCommentsFields.set(showUserCommentsFields);
     }
+
+    public void setPreviewWidthDividerPosition(double previewWidthDividerPosition) {
+        this.previewWidthDividerPosition.set(previewWidthDividerPosition);
+    }
+
+    /**
+     * Holds the horizontal divider position when the Preview is shown in the entry editor
+     */
+    public DoubleProperty previewWidthDividerPositionProperty() {
+        return previewWidthDividerPosition;
+    }
+
+    public Double getPreviewWidthDividerPosition() {
+        return previewWidthDividerPosition.get();
+    }
 }
diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
index 20e54396bfe..97348f5838a 100644
--- a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -41,6 +41,7 @@
 import org.jabref.preferences.PreferencesService;
 
 import com.tobiasdiez.easybind.EasyBind;
+import com.tobiasdiez.easybind.Subscription;
 
 /**
  * A single tab displayed in the EntryEditor holding several FieldEditors.
@@ -61,6 +62,7 @@ abstract class FieldsEditorTab extends EntryEditorTab {
     private PreviewPanel previewPanel;
     private final UndoManager undoManager;
     private Collection<Field> fields = new ArrayList<>();
+    private Subscription dividerPositionSubscription;
 
     public FieldsEditorTab(boolean compressed,
                            BibDatabaseContext databaseContext,
@@ -258,9 +260,22 @@ private void initPanel() {
                     container.getItems().remove(previewPanel);
                 } else {
                     container.getItems().add(1, previewPanel);
+                    container.setDividerPositions(preferences.getEntryEditorPreferences().getPreviewWidthDividerPosition());
                 }
             });
+
+            // save position
+            dividerPositionSubscription = EasyBind.valueAt(container.getDividers(), 0)
+                                                  .mapObservable(SplitPane.Divider::positionProperty)
+                                                  .subscribeToValues(this::savePreviewWidthDividerPosition);
             setContent(container);
         }
     }
+
+    private void savePreviewWidthDividerPosition(Number position) {
+        if (!preferences.getPreviewPreferences().shouldShowPreviewAsExtraTab()) {
+            preferences.getEntryEditorPreferences().setPreviewWidthDividerPosition(position.doubleValue());
+        }
+    }
 }
+
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index d9c747b3a1e..59b01569a34 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -173,6 +173,10 @@ public class JabRefPreferences implements PreferencesService {
     public static final String BIBLATEX_DEFAULT_MODE = "biblatexMode";
     public static final String NAMES_AS_IS = "namesAsIs";
     public static final String ENTRY_EDITOR_HEIGHT = "entryEditorHeightFX";
+    /**
+     *  Holds the horizontal divider position of the preview view when it is shown inside the entry editor
+     */
+    public static final String ENTRY_EDITOR_PREVIEW_DIVIDER_POS = "entryEditorPreviewDividerPos";
     public static final String AUTO_RESIZE_MODE = "autoResizeMode";
     public static final String WINDOW_MAXIMISED = "windowMaximised";
     public static final String WINDOW_FULLSCREEN = "windowFullscreen";
@@ -602,6 +606,7 @@ private JabRefPreferences() {
         defaults.put(WINDOW_FULLSCREEN, Boolean.FALSE);
         defaults.put(AUTO_RESIZE_MODE, Boolean.FALSE); // By default disable "Fit table horizontally on the screen"
         defaults.put(ENTRY_EDITOR_HEIGHT, 0.65);
+        defaults.put(ENTRY_EDITOR_PREVIEW_DIVIDER_POS, 0.5);
         defaults.put(NAMES_AS_IS, Boolean.FALSE); // "Show names unchanged"
         defaults.put(NAMES_FIRST_LAST, Boolean.FALSE); // "Show 'Firstname Lastname'"
         defaults.put(NAMES_NATBIB, Boolean.TRUE); // "Natbib style"
@@ -1488,7 +1493,8 @@ public EntryEditorPreferences getEntryEditorPreferences() {
                 getBoolean(AUTOLINK_FILES_ENABLED),
                 EntryEditorPreferences.JournalPopupEnabled.fromString(get(JOURNAL_POPUP)),
                 getBoolean(SHOW_SCITE_TAB),
-                getBoolean(SHOW_USER_COMMENTS_FIELDS));
+                getBoolean(SHOW_USER_COMMENTS_FIELDS),
+                getDouble(ENTRY_EDITOR_PREVIEW_DIVIDER_POS));
 
         EasyBind.listen(entryEditorPreferences.entryEditorTabs(), (obs, oldValue, newValue) -> storeEntryEditorTabs(newValue));
         // defaultEntryEditorTabs are read-only
@@ -1503,7 +1509,7 @@ public EntryEditorPreferences getEntryEditorPreferences() {
         EasyBind.listen(entryEditorPreferences.enableJournalPopupProperty(), (obs, oldValue, newValue) -> put(JOURNAL_POPUP, newValue.toString()));
         EasyBind.listen(entryEditorPreferences.shouldShowLSciteTabProperty(), (obs, oldValue, newValue) -> putBoolean(SHOW_SCITE_TAB, newValue));
         EasyBind.listen(entryEditorPreferences.showUserCommentsFieldsProperty(), (obs, oldValue, newValue) -> putBoolean(SHOW_USER_COMMENTS_FIELDS, newValue));
-
+        EasyBind.listen(entryEditorPreferences.previewWidthDividerPositionProperty(), (obs, oldValue, newValue) -> putDouble(ENTRY_EDITOR_PREVIEW_DIVIDER_POS, newValue.doubleValue()));
         return entryEditorPreferences;
     }
 

From 71efec0e1e222e4944b79680b7232c7ed4825dd3 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 12 May 2024 12:57:42 +0200
Subject: [PATCH 41/54] Try parallel tests (#9797)

* Try parallel tests

* Try to have "normal tests" running with 1 fork only

* Fix typo
---
 build.gradle | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/build.gradle b/build.gradle
index 6466119ed31..5095d6e76b4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -525,16 +525,32 @@ testlogger {
     showStackTraces false
 }
 
+tasks.withType(Test) {
+    reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
+    // Enable parallel tests. See https://docs.gradle.org/8.1/userguide/performance.html#execute_tests_in_parallel for details.
+    maxParallelForks = Runtime.runtime.availableProcessors() - 1
+}
+
 tasks.register('databaseTest', Test) {
     useJUnitPlatform {
         includeTags 'DatabaseTest'
     }
+
+    testLogging {
+        // set options for log level LIFECYCLE
+        events = ["FAILED"]
+        exceptionFormat "full"
+    }
+
+    maxParallelForks = 1
 }
 
 tasks.register('fetcherTest', Test) {
     useJUnitPlatform {
         includeTags 'FetcherTest'
     }
+
+    maxParallelForks = 1
 }
 
 tasks.register('guiTest', Test) {
@@ -547,6 +563,8 @@ tasks.register('guiTest', Test) {
         events = ["FAILED"]
         exceptionFormat "full"
     }
+
+    maxParallelForks = 1
 }
 
 // Test result tasks
@@ -556,10 +574,6 @@ tasks.register('copyTestResources', Copy) {
 }
 processTestResources.dependsOn copyTestResources
 
-tasks.withType(Test) {
-    reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
-}
-
 tasks.register('jacocoPrepare') {
     doFirst {
         // Ignore failures of tests

From 0eab5dcdf3c6ce37944e38025a11c83749517ba5 Mon Sep 17 00:00:00 2001
From: Rohit Garga <134286153+rohit-garga@users.noreply.github.com>
Date: Mon, 13 May 2024 14:30:18 +0530
Subject: [PATCH 42/54] Introduce formatter to remove word-enclosing braces
 (#11253)

* #11222 fix

* checkstyle fixes

* fixes for unit tests

* Make new RemoveWordEnclosingAndOuterEnclosingBracesFormatter available

* Add more braces to the example input

* Keep original string when formatting empty string

* Fix RemoveWordEnclosingAndOuterEnclosingBracesFormatter in the case of }} at the end

* Fix constant (and empty line)

* Reorder methods

* Add CHANGELOG.md entry

* markdown issue fix

* checkstyle fix

* duplicate keys issue fix

* author class not being initialized fix

* reverting key name change for old formatter

* reverting commit- Keep original string when formatting empty string since it causes unit tests to fail

* minor fixes

* minor fixes

* minor fixes

* fix: rewrite

* formatting fix

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
---
 CHANGELOG.md                                  |   1 +
 .../jabref/logic/formatter/Formatters.java    |   6 +-
 ...va => RemoveEnclosingBracesFormatter.java} |  22 +--
 ...osingAndOuterEnclosingBracesFormatter.java | 110 +++++++++++++++
 .../fetcher/AstrophysicsDataSystem.java       |   6 +-
 .../logic/importer/fetcher/CrossRef.java      |   4 +-
 .../importer/fetcher/INSPIREFetcher.java      |   4 +-
 .../jabref/logic/importer/fetcher/ZbMATH.java |   6 +-
 .../jabref/logic/msbib/MSBibConverter.java    |   4 +-
 .../org/jabref/logic/msbib/MsBibAuthor.java   |   4 +-
 .../style/OOBibStyleGetCitationMarker.java    |   4 +-
 .../java/org/jabref/model/entry/Author.java   | 125 +++++-------------
 src/main/resources/l10n/JabRef_en.properties  |   2 +
 ...> RemoveEnclosingBracesFormatterTest.java} |   4 +-
 ...gAndOuterEnclosingBracesFormatterTest.java |  31 +++++
 15 files changed, 208 insertions(+), 125 deletions(-)
 rename src/main/java/org/jabref/logic/formatter/bibtexfields/{RemoveBracesFormatter.java => RemoveEnclosingBracesFormatter.java} (97%)
 create mode 100644 src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatter.java
 rename src/test/java/org/jabref/logic/formatter/bibtexfields/{RemoveBracesFormatterTest.java => RemoveEnclosingBracesFormatterTest.java} (90%)
 create mode 100644 src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatterTest.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b972f15d2cc..a2cc933da15 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added value selection (such as for month) for content selectors in custom entry types. [#11109](https://github.com/JabRef/jabref/issues/11109)
 - We added a duplicate checker for the Citation Relations tab. [#10414](https://github.com/JabRef/jabref/issues/10414)
 - We added tooltip on main table cells that shows cell content or cell content and entry preview if set in preferences. [10925](https://github.com/JabRef/jabref/issues/10925)
+- Added a formatter to remove word enclosing braces. [#11222](https://github.com/JabRef/jabref/issues/11222)
 - We added the ability to add a keyword/crossref when typing the separator character (e.g., comma) in the keywords/crossref fields. [#11178](https://github.com/JabRef/jabref/issues/11178)
 - We added an exporter and improved the importer for Endnote XML format. [#11137](https://github.com/JabRef/jabref/issues/11137)
 - We added support for automatically update LaTeX citations when a LaTeX file is created, removed, or modified. [#10585](https://github.com/JabRef/jabref/issues/10585)
diff --git a/src/main/java/org/jabref/logic/formatter/Formatters.java b/src/main/java/org/jabref/logic/formatter/Formatters.java
index bcc7c202295..fb827f9ab8e 100644
--- a/src/main/java/org/jabref/logic/formatter/Formatters.java
+++ b/src/main/java/org/jabref/logic/formatter/Formatters.java
@@ -25,7 +25,8 @@
 import org.jabref.logic.formatter.bibtexfields.NormalizeUnicodeFormatter;
 import org.jabref.logic.formatter.bibtexfields.OrdinalsToSuperscriptFormatter;
 import org.jabref.logic.formatter.bibtexfields.RegexFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveWordEnclosingAndOuterEnclosingBracesFormatter;
 import org.jabref.logic.formatter.bibtexfields.ShortenDOIFormatter;
 import org.jabref.logic.formatter.bibtexfields.UnicodeToLatexFormatter;
 import org.jabref.logic.formatter.bibtexfields.UnitsToLatexFormatter;
@@ -82,7 +83,8 @@ public static List<Formatter> getOthers() {
                 new NormalizeNamesFormatter(),
                 new NormalizePagesFormatter(),
                 new OrdinalsToSuperscriptFormatter(),
-                new RemoveBracesFormatter(),
+                new RemoveEnclosingBracesFormatter(),
+                new RemoveWordEnclosingAndOuterEnclosingBracesFormatter(),
                 new UnitsToLatexFormatter(),
                 new EscapeUnderscoresFormatter(),
                 new EscapeAmpersandsFormatter(),
diff --git a/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatter.java b/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatter.java
similarity index 97%
rename from src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatter.java
rename to src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatter.java
index c29b081cc48..31b071aac12 100644
--- a/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatter.java
+++ b/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatter.java
@@ -6,7 +6,7 @@
 import org.jspecify.annotations.NullMarked;
 
 @NullMarked
-public class RemoveBracesFormatter extends Formatter {
+public class RemoveEnclosingBracesFormatter extends Formatter {
 
     @Override
     public String getName() {
@@ -18,6 +18,16 @@ public String getKey() {
         return "remove_braces";
     }
 
+    @Override
+    public String getDescription() {
+        return Localization.lang("Removes braces encapsulating the complete field content.");
+    }
+
+    @Override
+    public String getExampleInput() {
+        return "{In CDMA}";
+    }
+
     @Override
     public String format(String value) {
         String formatted = value;
@@ -37,16 +47,6 @@ public String format(String value) {
         return formatted;
     }
 
-    @Override
-    public String getDescription() {
-        return Localization.lang("Removes braces encapsulating the complete field content.");
-    }
-
-    @Override
-    public String getExampleInput() {
-        return "{In CDMA}";
-    }
-
     /**
      * Check if a string at any point has had more ending } braces than opening { ones.
      * Will e.g. return true for the string "DNA} text {EPA"
diff --git a/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatter.java b/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatter.java
new file mode 100644
index 00000000000..c70c7315ebe
--- /dev/null
+++ b/src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatter.java
@@ -0,0 +1,110 @@
+package org.jabref.logic.formatter.bibtexfields;
+
+import java.util.Objects;
+import java.util.StringJoiner;
+
+import org.jabref.logic.cleanup.Formatter;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.strings.StringUtil;
+
+import org.jspecify.annotations.NullMarked;
+
+/**
+ * Removes start and end brace both at the complete string and at beginning/end of a word
+ * <p>
+ * E.g.,
+ * <ul>
+ *     <li>{Vall{\'e}e Poussin} -> Vall{\'e}e Poussin</li>
+ *     <li>{Vall{\'e}e} {Poussin} -> Vall{\'e}e Poussin</li>
+ *     <li>Vall{\'e}e Poussin -> Vall{\'e}e Poussin</li>
+ * </ul>
+ */
+@NullMarked
+public class RemoveWordEnclosingAndOuterEnclosingBracesFormatter extends Formatter {
+
+    private static final RemoveEnclosingBracesFormatter REMOVE_ENCLOSING_BRACES_FORMATTER = new RemoveEnclosingBracesFormatter();
+
+    @Override
+    public String getName() {
+        return Localization.lang("Remove word enclosing braces");
+    }
+
+    @Override
+    public String getKey() {
+        return "remove_enclosing_and_outer_enclosing_braces";
+    }
+
+    @Override
+    public String getDescription() {
+        return Localization.lang("Removes braces encapsulating a complete word and the complete field content.");
+    }
+
+    @Override
+    public String getExampleInput() {
+        return "{In {CDMA}}";
+    }
+
+    @Override
+    public String format(String input) {
+        Objects.requireNonNull(input);
+        if (StringUtil.isBlank(input)) {
+            return input;
+        }
+
+        if (!input.contains("{")) {
+            return input;
+        }
+
+        // We need to first remove the outer braces to have double braces at the last word working (e.g., {In {CDMA}})
+        input = REMOVE_ENCLOSING_BRACES_FORMATTER.format(input);
+
+        String[] split = input.split(" ");
+        StringJoiner result = new StringJoiner(" ");
+        for (String s : split) {
+            if ((s.length() > 2) && s.startsWith("{") && s.endsWith("}")) {
+                // quick solution (which we don't do): just remove first "{" and last "}"
+                // however, it might be that s is like {A}bbb{c}, where braces may not be removed
+
+                String inner = s.substring(1, s.length() - 1);
+
+                if (inner.contains("}")) {
+                    if (properBrackets(inner)) {
+                        s = inner;
+                    }
+                } else {
+                    //  no inner curly brackets found, no check needed, inner can just be used as s
+                    s = inner;
+                }
+            }
+            result.add(s);
+        }
+        return result.toString();
+    }
+
+    /**
+     * @return true iff the brackets in s are properly paired
+     */
+    private boolean properBrackets(String s) {
+        // nested construct is there, check for "proper" nesting
+        int i = 0;
+        int level = 0;
+        while (i < s.length()) {
+            char c = s.charAt(i);
+            switch (c) {
+                case '{':
+                    level++;
+                    break;
+                case '}':
+                    level--;
+                    if (level == -1) { // improper nesting
+                        return false;
+                    }
+                    break;
+                default:
+                    break;
+            }
+            i++;
+        }
+        return level == 0;
+    }
+}
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java b/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java
index 7b85d1534cd..23e5c077d8b 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java
@@ -17,7 +17,7 @@
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeMonthFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.logic.formatter.bibtexfields.RemoveNewlinesFormatter;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.EntryBasedParserFetcher;
@@ -149,9 +149,9 @@ public Parser getParser() {
 
     @Override
     public void doPostCleanup(BibEntry entry) {
-        new FieldFormatterCleanup(StandardField.ABSTRACT, new RemoveBracesFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(StandardField.ABSTRACT, new RemoveEnclosingBracesFormatter()).cleanup(entry);
         new FieldFormatterCleanup(StandardField.ABSTRACT, new RemoveNewlinesFormatter()).cleanup(entry);
-        new FieldFormatterCleanup(StandardField.TITLE, new RemoveBracesFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(StandardField.TITLE, new RemoveEnclosingBracesFormatter()).cleanup(entry);
         new FieldFormatterCleanup(StandardField.AUTHOR, new NormalizeNamesFormatter()).cleanup(entry);
         new FieldFormatterCleanup(StandardField.MONTH, new NormalizeMonthFormatter()).cleanup(entry);
 
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java b/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java
index 4826239e3e6..c34277add1e 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java
@@ -11,7 +11,7 @@
 
 import org.jabref.logic.cleanup.FieldFormatterCleanup;
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.logic.importer.EntryBasedParserFetcher;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedParserFetcher;
@@ -46,7 +46,7 @@ public class CrossRef implements IdParserFetcher<DOI>, EntryBasedParserFetcher,
 
     private static final String API_URL = "https://api.crossref.org/works";
 
-    private static final RemoveBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveBracesFormatter();
+    private static final RemoveEnclosingBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveEnclosingBracesFormatter();
 
     @Override
     public String getName() {
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/INSPIREFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/INSPIREFetcher.java
index 67f9e84afc0..86d27594a84 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/INSPIREFetcher.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/INSPIREFetcher.java
@@ -11,7 +11,7 @@
 
 import org.jabref.logic.cleanup.FieldFormatterCleanup;
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.EntryBasedFetcher;
 import org.jabref.logic.importer.FetcherException;
@@ -76,7 +76,7 @@ public void doPostCleanup(BibEntry entry) {
         new FieldFormatterCleanup(new UnknownField("SLACcitation"), new ClearFormatter()).cleanup(entry);
 
         // Remove braces around content of "title" field
-        new FieldFormatterCleanup(StandardField.TITLE, new RemoveBracesFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(StandardField.TITLE, new RemoveEnclosingBracesFormatter()).cleanup(entry);
 
         new FieldFormatterCleanup(StandardField.TITLE, new LatexToUnicodeFormatter()).cleanup(entry);
     }
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/ZbMATH.java b/src/main/java/org/jabref/logic/importer/fetcher/ZbMATH.java
index 70afa7847c1..c8398a1e8f3 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/ZbMATH.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/ZbMATH.java
@@ -9,7 +9,7 @@
 
 import org.jabref.logic.cleanup.FieldFormatterCleanup;
 import org.jabref.logic.cleanup.MoveFieldCleanup;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.logic.importer.EntryBasedParserFetcher;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedParserFetcher;
@@ -131,7 +131,7 @@ public Parser getParser() {
     public void doPostCleanup(BibEntry entry) {
         new MoveFieldCleanup(new UnknownField("msc2010"), StandardField.KEYWORDS).cleanup(entry);
         new MoveFieldCleanup(AMSField.FJOURNAL, StandardField.JOURNAL).cleanup(entry);
-        new FieldFormatterCleanup(StandardField.JOURNAL, new RemoveBracesFormatter()).cleanup(entry);
-        new FieldFormatterCleanup(StandardField.TITLE, new RemoveBracesFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(StandardField.JOURNAL, new RemoveEnclosingBracesFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(StandardField.TITLE, new RemoveEnclosingBracesFormatter()).cleanup(entry);
     }
 }
diff --git a/src/main/java/org/jabref/logic/msbib/MSBibConverter.java b/src/main/java/org/jabref/logic/msbib/MSBibConverter.java
index d565195e6fc..1870254e933 100644
--- a/src/main/java/org/jabref/logic/msbib/MSBibConverter.java
+++ b/src/main/java/org/jabref/logic/msbib/MSBibConverter.java
@@ -4,7 +4,7 @@
 import java.util.List;
 import java.util.Optional;
 
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.Month;
@@ -18,7 +18,7 @@ public class MSBibConverter {
 
     private static final String MSBIB_PREFIX = "msbib-";
     private static final String BIBTEX_PREFIX = "BIBTEX_";
-    private static final RemoveBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveBracesFormatter();
+    private static final RemoveEnclosingBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveEnclosingBracesFormatter();
 
     private MSBibConverter() {
     }
diff --git a/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java b/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
index bcceef9657f..9285a4d9d05 100644
--- a/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
+++ b/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
@@ -1,11 +1,11 @@
 package org.jabref.logic.msbib;
 
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.model.entry.Author;
 
 public class MsBibAuthor {
 
-    private static final RemoveBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveBracesFormatter();
+    private static final RemoveEnclosingBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveEnclosingBracesFormatter();
 
     private String firstName;
     private String middleName;
diff --git a/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetCitationMarker.java b/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetCitationMarker.java
index c38e3d37ed0..aff4c1ce84c 100644
--- a/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetCitationMarker.java
+++ b/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetCitationMarker.java
@@ -5,7 +5,7 @@
 import java.util.List;
 import java.util.Optional;
 
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.Author;
 import org.jabref.model.entry.AuthorList;
@@ -24,7 +24,7 @@
 
 class OOBibStyleGetCitationMarker {
 
-    private static final RemoveBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveBracesFormatter();
+    private static final RemoveEnclosingBracesFormatter REMOVE_BRACES_FORMATTER = new RemoveEnclosingBracesFormatter();
 
     private OOBibStyleGetCitationMarker() {
     }
diff --git a/src/main/java/org/jabref/model/entry/Author.java b/src/main/java/org/jabref/model/entry/Author.java
index e4511e7ef07..5892ca0b457 100644
--- a/src/main/java/org/jabref/model/entry/Author.java
+++ b/src/main/java/org/jabref/model/entry/Author.java
@@ -3,6 +3,8 @@
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.architecture.AllowedToUseLogic;
+import org.jabref.logic.formatter.bibtexfields.RemoveWordEnclosingAndOuterEnclosingBracesFormatter;
 import org.jabref.model.strings.LatexToUnicodeAdapter;
 import org.jabref.model.strings.StringUtil;
 
@@ -11,6 +13,7 @@
  * <p>
  * Current usage: only methods <code>getLastOnly</code>, <code>getFirstLast</code>, and <code>getLastFirst</code> are used; all other methods are provided for completeness.
  */
+@AllowedToUseLogic("because it needs to use formatter")
 public class Author {
 
     /**
@@ -20,6 +23,8 @@ public class Author {
      */
     public static final Author OTHERS = new Author("", "", null, "others", null);
 
+    public static final RemoveWordEnclosingAndOuterEnclosingBracesFormatter FORMATTER = new RemoveWordEnclosingAndOuterEnclosingBracesFormatter();
+
     private final String givenName;
     private final String givenNameAbbreviated;
     private final String namePrefix;
@@ -41,17 +46,37 @@ public class Author {
     public Author(String givenName, String givenNameAbbreviated, String namePrefix, String familyName, String nameSuffix) {
         boolean keepBracesAtLastPart = StringUtil.isBlank(givenName) && StringUtil.isBlank(givenNameAbbreviated) && StringUtil.isBlank(namePrefix) && !StringUtil.isBlank(familyName) && StringUtil.isBlank(nameSuffix);
 
-        this.givenName = addDotIfAbbreviation(removeStartAndEndBraces(givenName));
-        this.givenNameAbbreviated = removeStartAndEndBraces(givenNameAbbreviated);
-        this.namePrefix = removeStartAndEndBraces(namePrefix);
+        if (!StringUtil.isBlank(givenName)) {
+            this.givenName = addDotIfAbbreviation(FORMATTER.format(givenName));
+        } else {
+            this.givenName = null;
+        }
+        if (!StringUtil.isBlank(givenNameAbbreviated)) {
+            this.givenNameAbbreviated = FORMATTER.format(givenNameAbbreviated);
+        } else {
+            this.givenNameAbbreviated = null;
+        }
+        if (!StringUtil.isBlank(namePrefix)) {
+            this.namePrefix = FORMATTER.format(namePrefix);
+        } else {
+            this.namePrefix = null;
+        }
         if (keepBracesAtLastPart) {
             // We do not remove braces here to keep institutions protected
             // https://github.com/JabRef/jabref/issues/10031
             this.familyName = familyName;
         } else {
-            this.familyName = removeStartAndEndBraces(familyName);
+            if (!StringUtil.isBlank(familyName)) {
+                this.familyName = FORMATTER.format(familyName);
+            } else {
+                this.familyName = null;
+            }
+        }
+        if (!StringUtil.isBlank(nameSuffix)) {
+            this.nameSuffix = FORMATTER.format(nameSuffix);
+        } else {
+            this.nameSuffix = null;
         }
-        this.nameSuffix = removeStartAndEndBraces(nameSuffix);
     }
 
     public static String addDotIfAbbreviation(String name) {
@@ -165,94 +190,6 @@ public boolean equals(Object other) {
         return false;
     }
 
-    /**
-     * @return true iff the brackets in s are properly paired
-     */
-    private boolean properBrackets(String s) {
-        // nested construct is there, check for "proper" nesting
-        int i = 0;
-        int level = 0;
-        while (i < s.length()) {
-            char c = s.charAt(i);
-            switch (c) {
-                case '{':
-                    level++;
-                    break;
-                case '}':
-                    level--;
-                    if (level == -1) { // improper nesting
-                        return false;
-                    }
-                    break;
-                default:
-                    break;
-            }
-            i++;
-        }
-        return level == 0;
-    }
-
-    /**
-     * Removes start and end brace both at the complete string and at beginning/end of a word
-     * <p>
-     * E.g.,
-     * <ul>
-     *     <li>{Vall{\'e}e Poussin} -> Vall{\'e}e Poussin</li>
-     *     <li>{Vall{\'e}e} {Poussin} -> Vall{\'e}e Poussin</li>
-     *     <li>Vall{\'e}e Poussin -> Vall{\'e}e Poussin</li>
-     * </ul>
-     */
-    private String removeStartAndEndBraces(String name) {
-        if (StringUtil.isBlank(name)) {
-            return null;
-        }
-
-        if (!name.contains("{")) {
-            return name;
-        }
-
-        String[] split = name.split(" ");
-        StringBuilder b = new StringBuilder();
-        for (String s : split) {
-            if ((s.length() > 2) && s.startsWith("{") && s.endsWith("}")) {
-                // quick solution (which we don't do: just remove first "{" and last "}"
-                // however, it might be that s is like {A}bbb{c}, where braces may not be removed
-
-                // inner
-                String inner = s.substring(1, s.length() - 1);
-
-                if (inner.contains("}")) {
-                    if (properBrackets(inner)) {
-                        s = inner;
-                    }
-                } else {
-                    //  no inner curly brackets found, no check needed, inner can just be used as s
-                    s = inner;
-                }
-            }
-            b.append(s).append(' ');
-        }
-        // delete last
-        b.deleteCharAt(b.length() - 1);
-
-        // now, all inner words are cleared
-        // case {word word word} remains
-        // as above, we have to be aware of {w}ord word wor{d} and {{w}ord word word}
-
-        String newName = b.toString();
-
-        if (newName.startsWith("{") && newName.endsWith("}")) {
-            String inner = newName.substring(1, newName.length() - 1);
-            if (properBrackets(inner)) {
-                return inner;
-            } else {
-                return newName;
-            }
-        } else {
-            return newName;
-        }
-    }
-
     /**
      * Returns the first name of the author stored in this object ("First").
      *
@@ -304,7 +241,7 @@ public Optional<String> getNameSuffix() {
      * @return 'von Last'
      */
     public String getNamePrefixAndFamilyName() {
-        if (namePrefix == null) {
+        if (namePrefix == null || "".equals(namePrefix)) {
             return getFamilyName().orElse("");
         } else {
             return familyName == null ? namePrefix : namePrefix + ' ' + familyName;
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index b8326bbbe12..21c49a26efb 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1480,6 +1480,8 @@ Protect\ terms=Protect terms
 Add\ enclosing\ braces=Add enclosing braces
 Add\ braces\ encapsulating\ the\ complete\ field\ content.=Add braces encapsulating the complete field content.
 Remove\ enclosing\ braces=Remove enclosing braces
+Remove\ word\ enclosing\ braces=Remove word enclosing braces
+Removes\ braces\ encapsulating\ a\ complete\ word\ and\ the\ complete\ field\ content.=Removes braces encapsulating a complete word and the complete field content.
 Removes\ braces\ encapsulating\ the\ complete\ field\ content.=Removes braces encapsulating the complete field content.
 Removes\ all\ balanced\ {}\ braces\ around\ words.=Removes all balanced {} braces around words.
 Shorten\ DOI=Shorten DOI
diff --git a/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatterTest.java b/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatterTest.java
similarity index 90%
rename from src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatterTest.java
rename to src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatterTest.java
index 37eff160e67..45f6e87373d 100644
--- a/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatterTest.java
+++ b/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatterTest.java
@@ -9,9 +9,9 @@
 /**
  * Tests in addition to the general tests from {@link org.jabref.logic.formatter.FormatterTest}
  */
-public class RemoveBracesFormatterTest {
+public class RemoveEnclosingBracesFormatterTest {
 
-    private final RemoveBracesFormatter formatter = new RemoveBracesFormatter();
+    private final RemoveEnclosingBracesFormatter formatter = new RemoveEnclosingBracesFormatter();
 
     @ParameterizedTest
     @CsvSource({
diff --git a/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatterTest.java b/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatterTest.java
new file mode 100644
index 00000000000..036268c7929
--- /dev/null
+++ b/src/test/java/org/jabref/logic/formatter/bibtexfields/RemoveWordEnclosingAndOuterEnclosingBracesFormatterTest.java
@@ -0,0 +1,31 @@
+package org.jabref.logic.formatter.bibtexfields;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class RemoveWordEnclosingAndOuterEnclosingBracesFormatterTest {
+    private final RemoveWordEnclosingAndOuterEnclosingBracesFormatter formatter = new RemoveWordEnclosingAndOuterEnclosingBracesFormatter();
+
+    @ParameterizedTest
+    @CsvSource({
+            "A test B, {A} test {B}",
+            "A and B, {{A} and {B}}",
+            "{w}ord word wor{d}, {w}ord word wor{d}",
+            "{w}ord word word, {{w}ord word word}",
+            "{w}ord word wor{d}, {w}ord word {wor{d}}",
+            "Vall{\\'e}e Poussin, {Vall{\\'e}e} {Poussin}",
+            "Vall{\\'e}e Poussin, {Vall{\\'e}e Poussin}",
+            "Vall{\\'e}e Poussin, Vall{\\'e}e Poussin"
+    })
+    public void format(String expected, String input) {
+        assertEquals(expected, formatter.format(input));
+    }
+
+    @Test
+    public void formatExample() {
+        assertEquals("In CDMA", formatter.format(formatter.getExampleInput()));
+    }
+}

From efc60e8b83f84aa29996ee47ecd51e8078dc1987 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 14:32:36 +0000
Subject: [PATCH 43/54] Bump org.openrewrite.recipe:rewrite-recipe-bom from
 2.9.0 to 2.11.0 (#11288)

Bumps [org.openrewrite.recipe:rewrite-recipe-bom](https://github.com/openrewrite/rewrite-recipe-bom) from 2.9.0 to 2.11.0.
- [Release notes](https://github.com/openrewrite/rewrite-recipe-bom/releases)
- [Commits](https://github.com/openrewrite/rewrite-recipe-bom/compare/v2.9.0...v2.11.0)

---
updated-dependencies:
- dependency-name: org.openrewrite.recipe:rewrite-recipe-bom
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 5095d6e76b4..2c481dbe9e9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -316,7 +316,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.9.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.11.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

From ebee05b743348ce36b76efa1a087f161ad66adb2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 14:32:44 +0000
Subject: [PATCH 44/54] Bump com.dlsc.gemsfx:gemsfx from 2.12.0 to 2.16.0
 (#11287)

Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.12.0 to 2.16.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/jreleaser.yml)
- [Commits](https://github.com/dlsc-software-consulting-gmbh/GemsFX/compare/v2.12.0...v2.16.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 2c481dbe9e9..269f26fa278 100644
--- a/build.gradle
+++ b/build.gradle
@@ -218,7 +218,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.12.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.16.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.openjfx'

From 7aacd76931155db83a1774d6988027390bccc8b2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 14:34:25 +0000
Subject: [PATCH 45/54] Bump
 com.fasterxml.jackson.datatype:jackson-datatype-jsr310 (#11289)

Bumps com.fasterxml.jackson.datatype:jackson-datatype-jsr310 from 2.17.0 to 2.17.1.

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.datatype:jackson-datatype-jsr310
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 269f26fa278..93de7feab05 100644
--- a/build.gradle
+++ b/build.gradle
@@ -185,7 +185,7 @@ dependencies {
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.9.0.202403050737-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.0'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.0'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.1'
 
     implementation 'com.fasterxml:aalto-xml:1.3.2'
 

From 5077e9a8e6f239fc697718472a29e75a6f13bc9a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 14:40:54 +0000
Subject: [PATCH 46/54] Bump org.mockito:mockito-core from 5.11.0 to 5.12.0
 (#11291)

Bumps [org.mockito:mockito-core](https://github.com/mockito/mockito) from 5.11.0 to 5.12.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v5.11.0...v5.12.0)

---
updated-dependencies:
- dependency-name: org.mockito:mockito-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 93de7feab05..7db0adec82c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -302,7 +302,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
-    testImplementation 'org.mockito:mockito-core:5.11.0'
+    testImplementation 'org.mockito:mockito-core:5.12.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'

From fa13c6ecb6f3f5758d8918a6301a9abfe1e59382 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 14:49:22 +0000
Subject: [PATCH 47/54] Bump src/main/resources/csl-styles from `5338902` to
 `434df0a` (#11292)

Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `5338902` to `434df0a`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](https://github.com/citation-style-language/styles/compare/533890226e8abbbeb31cd63a5b1180ffc6e4870d...434df0ad75d7416bb651ad1f08826a5152c77a27)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-styles
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 src/main/resources/csl-styles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
index 533890226e8..434df0ad75d 160000
--- a/src/main/resources/csl-styles
+++ b/src/main/resources/csl-styles
@@ -1 +1 @@
-Subproject commit 533890226e8abbbeb31cd63a5b1180ffc6e4870d
+Subproject commit 434df0ad75d7416bb651ad1f08826a5152c77a27

From 708b4c7ca6c4a528c67282cfcf5bfd981f1bd27b Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Mon, 13 May 2024 21:50:11 +0300
Subject: [PATCH 48/54] Remove outdated pdf indexed files from Lucene index
 (#11293)

---
 .../org/jabref/logic/pdf/search/PdfIndexer.java     | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
index 7b66b1c62ca..be3d5e8faf5 100644
--- a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
+++ b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
@@ -205,7 +205,7 @@ public void addToIndex(BibEntry entry, Collection<LinkedFile> linkedFiles, boole
 
     private void doCommit() {
         try {
-            getIndexWriter().ifPresent(Unchecked.consumer(writer -> writer.commit()));
+            getIndexWriter().ifPresent(Unchecked.consumer(IndexWriter::commit));
         } catch (UncheckedIOException e) {
             LOGGER.warn("Could not commit changes to the index.", e);
         }
@@ -274,7 +274,6 @@ private void addToIndex(BibEntry entry, LinkedFile linkedFile, boolean shouldCom
             LOGGER.debug("Could not find {}", linkedFile.getLink());
             return;
         }
-        LOGGER.debug("Adding {} to index", linkedFile.getLink());
         try {
             // Check if a document with this path is already in the index
             try {
@@ -283,17 +282,21 @@ private void addToIndex(BibEntry entry, LinkedFile linkedFile, boolean shouldCom
                 TopDocs topDocs = searcher.search(query, 1);
                 // If a document was found, check if is less current than the one in the FS
                 if (topDocs.scoreDocs.length > 0) {
-                    Document doc = reader.document(topDocs.scoreDocs[0].doc);
+                    Document doc = reader.storedFields().document(topDocs.scoreDocs[0].doc);
                     long indexModificationTime = Long.parseLong(doc.getField(SearchFieldConstants.MODIFIED).stringValue());
                     BasicFileAttributes attributes = Files.readAttributes(resolvedPath.get(), BasicFileAttributes.class);
                     if (indexModificationTime >= attributes.lastModifiedTime().to(TimeUnit.SECONDS)) {
-                        LOGGER.debug("File {} is already indexed", linkedFile.getLink());
+                        LOGGER.debug("File {} is already indexed and up-to-date.", linkedFile.getLink());
                         return;
+                    } else {
+                        LOGGER.debug("File {} is already indexed but outdated. Removing from index.", linkedFile.getLink());
+                        removeFromIndex(linkedFile.getLink());
                     }
                 }
             } catch (IndexNotFoundException e) {
                 LOGGER.debug("Index not found. Continuing.", e);
             }
+            LOGGER.debug("Adding {} to index", linkedFile.getLink());
             // If no document was found, add the new one
             Optional<List<Document>> pages = new DocumentReader(entry, filePreferences).readLinkedPdf(this.databaseContext, linkedFile);
             if (pages.isPresent()) {
@@ -328,7 +331,7 @@ public Set<String> getListOfFilePaths() {
             MatchAllDocsQuery query = new MatchAllDocsQuery();
             TopDocs allDocs = searcher.search(query, Integer.MAX_VALUE);
             for (ScoreDoc scoreDoc : allDocs.scoreDocs) {
-                Document doc = reader.document(scoreDoc.doc);
+                Document doc = reader.storedFields().document(scoreDoc.doc);
                 paths.add(doc.getField(SearchFieldConstants.PATH).stringValue());
             }
         } catch (IOException e) {

From 6376067faf44a7e24a5fabed03856586b17fe501 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 14 May 2024 09:13:20 +0200
Subject: [PATCH 49/54] Bump
 com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (#11290)

Bumps [com.fasterxml.jackson.dataformat:jackson-dataformat-yaml](https://github.com/FasterXML/jackson-dataformats-text) from 2.17.0 to 2.17.1.
- [Commits](https://github.com/FasterXML/jackson-dataformats-text/compare/jackson-dataformats-text-2.17.0...jackson-dataformats-text-2.17.1)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.dataformat:jackson-dataformat-yaml
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Christoph <siedlerkiller@gmail.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 7db0adec82c..f01129eab7b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -184,7 +184,7 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.9.0.202403050737-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.0'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.1'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.1'
 
     implementation 'com.fasterxml:aalto-xml:1.3.2'

From 2d179422ee7c55b01a02218e50d131d025ad62aa Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 14 May 2024 16:05:56 +0200
Subject: [PATCH 50/54] Remove obsolete step (#11295)

---
 ...guidelines-intellij-open-module-settings.png | Bin 68332 -> 0 bytes
 .../intellij-12-build.md                        |   6 ------
 2 files changed, 6 deletions(-)
 delete mode 100644 docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/guidelines-intellij-open-module-settings.png

diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/guidelines-intellij-open-module-settings.png b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/guidelines-intellij-open-module-settings.png
deleted file mode 100644
index deef5f86734870d8d929b44ec96116d2abecbedc..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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zBDLOIlxBE9deEz(un~8kIxqX?m0K>4A`mO*pCm7-VKa?r62-NK^Ix4hFPh^J_ep-U
zqgwFr;}sKH0%aPPmJJ+W5u%kHvL(@|XS9yuuKv5cJkkw@eyD?qej=;i6k|bj$v6I+
zTvgU1{Fep~!NYI=9j)+3R5Jd9v;D6NQo{j*K<<5DDV=i#^c4sM#RWAv&SH<S_B2BF
z<BS&&;V_1?pM+*2K!p|{nAZ8tFyhlik*F3nZgVZO|6sMk#NjpKKK128L`gw$J-tw>
z4=PU;Y-f+T)&_e@KDU#(zg?7a2Cj*}t4uU~95TB{<6qtzza8!J?E&2WW<4<t3!=;k
ztyg8Ua{EE~QN|rl2Nm%u*Wfk1CIQVCUBkTS7~zO~^tqbV@cJ7`O?fW~mC>$uv-?u@
zFP<tx=~t#Qez;sHux<Ww#rwS7mEhX5aKO%>Nz$BNq)jmS40<5QE->(|QxYX3X+HmD
zf9m?-I}#(Iu6;4{Z#?T7NQYSK*jGX^ZYR7qr@f3MWAebWVcVaugi_w`map5EJ_7a+
OfRyA^Ws9LE0sjTgItqvY

diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
index 1dfb4f01f58..3ffe0b5ca9c 100644
--- a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
+++ b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
@@ -32,12 +32,6 @@ After clicking "Download", IntelliJ installs Eclipse Temurin:
 ![IntelliJ installs Eclipse Temurin](guidelines-intellij-installs-temurin.png)
 {% endfigure %}
 
-Open the module settings: Right click on "JabRef" and select "Open Module Settings":
-
-{% figure caption:"Open IntelliJ Module Settings" %}
-![IntelliJ Module Settings](guidelines-intellij-open-module-settings.png)
-{% endfigure %}
-
 Navigate to **Project Settings > Project** and ensure that the projects' SDK is Java 21.
 
 {% figure caption:"Project SDK is pinned to the downloaded SDK (showing JDK 21 as example)" %}

From 3e1dbccfd557c02f39c499ad08aa15b2551f5b7b Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Fri, 17 May 2024 17:29:08 +0200
Subject: [PATCH 51/54] Try gradle build speedup (#11300)

---
 build.gradle      |  3 +++
 gradle.properties | 10 ++++++++++
 2 files changed, 13 insertions(+)

diff --git a/build.gradle b/build.gradle
index f01129eab7b..a545093ff9e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -424,6 +424,9 @@ tasks.register('generateCitaviSource', XjcTask) {
 
 tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
+
+    // hint by https://docs.gradle.org/current/userguide/performance.html#run_the_compiler_as_a_separate_process
+    options.fork = true
 }
 
 compileJava {
diff --git a/gradle.properties b/gradle.properties
index 8e7f633fecd..7de2be111f2 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,2 +1,12 @@
 org.gradle.vs.watch=true
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#increase_the_heap_size
 org.gradle.jvmargs=-Xmx4096M
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#enable_configuration_cache
+# Does not work:
+# - Task `:compileJava` of type `org.gradle.api.tasks.compile.JavaCompile`: cannot serialize object of type 'org.gradle.api.internal.project.DefaultProject', a subtype of 'org.gradle.api.Project', as these are not supported with the configuration cache.
+# org.gradle.configuration-cache=false
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#enable_the_build_cache
+org.gradle.caching=true

From 9fdc2946a1d23e089db4b691105e5311dd33372c Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Fri, 17 May 2024 17:29:49 +0200
Subject: [PATCH 52/54] Fix comment (#11299)

---
 src/main/java/org/jabref/model/entry/BibEntry.java | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
index 6f463422a36..b52b827579f 100644
--- a/src/main/java/org/jabref/model/entry/BibEntry.java
+++ b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -45,6 +45,7 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.MultiKeyMap;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.eventbus.EventBus;
 import com.tobiasdiez.easybind.EasyBind;
 import com.tobiasdiez.easybind.optional.OptionalBinding;
@@ -353,19 +354,22 @@ private Optional<String> genericGetResolvedFieldOrAlias(Field field, BibDatabase
     }
 
     /**
-     * Returns this entry's ID.
+     * Returns this entry's ID. It is used internally to distinguish different BibTeX entries.
+     * <p>
+     * It is <emph>not</emph> the citation key (which is stored in the {@link InternalField#KEY_FIELD} and also known as BibTeX key).
      */
     public String getId() {
         return id;
     }
 
     /**
-     * Sets this entry's identifier (ID). It is used internally  to distinguish different BibTeX entries. It is <emph>not</emph> the citation key. The BibTexKey is the {@link InternalField#KEY_FIELD}.
+     * Sets this entry's identifier (ID).
      * <p>
      * The entry is also updated in the shared database - provided the database containing it doesn't veto the change.
      *
      * @param id The ID to be used
      */
+    @VisibleForTesting
     public void setId(String id) {
         Objects.requireNonNull(id, "Every BibEntry must have an ID");
 

From b12f65c1de48572efd68cb4e8b2416e16cb61366 Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Fri, 17 May 2024 23:45:20 +0300
Subject: [PATCH 53/54] Remove EnglishStemAnalyzer and use EnglishAnalyzer
 (#11301)

---
 .../jabref/logic/pdf/search/PdfIndexer.java   |  4 +--
 .../jabref/logic/pdf/search/PdfSearcher.java  |  7 +++---
 .../model/pdf/search/EnglishStemAnalyzer.java | 25 -------------------
 .../jabref/model/pdf/search/SearchResult.java | 10 +++++---
 4 files changed, 13 insertions(+), 33 deletions(-)
 delete mode 100644 src/main/java/org/jabref/model/pdf/search/EnglishStemAnalyzer.java

diff --git a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
index be3d5e8faf5..45750ac5b84 100644
--- a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
+++ b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
@@ -16,11 +16,11 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.pdf.search.EnglishStemAnalyzer;
 import org.jabref.model.pdf.search.SearchFieldConstants;
 import org.jabref.preferences.FilePreferences;
 
 import com.google.common.annotations.VisibleForTesting;
+import org.apache.lucene.analysis.en.EnglishAnalyzer;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.IndexNotFoundException;
@@ -130,7 +130,7 @@ private void initializeIndexWriterAndReader(IndexWriterConfig.OpenMode mode) {
             indexWriter = new IndexWriter(
                     indexDirectory,
                     new IndexWriterConfig(
-                            new EnglishStemAnalyzer()).setOpenMode(mode));
+                            new EnglishAnalyzer()).setOpenMode(mode));
         } catch (IOException e) {
             LOGGER.error("Could not initialize the IndexWriter", e);
             // FIXME: This can also happen if another instance of JabRef is launched in parallel.
diff --git a/src/main/java/org/jabref/logic/pdf/search/PdfSearcher.java b/src/main/java/org/jabref/logic/pdf/search/PdfSearcher.java
index 40acc97f8af..fb6afccc29b 100644
--- a/src/main/java/org/jabref/logic/pdf/search/PdfSearcher.java
+++ b/src/main/java/org/jabref/logic/pdf/search/PdfSearcher.java
@@ -7,11 +7,12 @@
 import java.util.Optional;
 
 import org.jabref.gui.LibraryTab;
-import org.jabref.model.pdf.search.EnglishStemAnalyzer;
 import org.jabref.model.pdf.search.PdfSearchResults;
 import org.jabref.model.pdf.search.SearchResult;
 import org.jabref.model.strings.StringUtil;
 
+import org.apache.lucene.analysis.Analyzer;
+import org.apache.lucene.analysis.en.EnglishAnalyzer;
 import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.IndexReader;
 import org.apache.lucene.index.IndexWriter;
@@ -31,7 +32,7 @@ public final class PdfSearcher {
     private static final Logger LOGGER = LoggerFactory.getLogger(LibraryTab.class);
 
     private final PdfIndexer indexer;
-    private EnglishStemAnalyzer englishStemAnalyzer = new EnglishStemAnalyzer();
+    private final Analyzer englishAnalyzer = new EnglishAnalyzer();
 
     private PdfSearcher(PdfIndexer indexer) {
         this.indexer = indexer;
@@ -65,7 +66,7 @@ public PdfSearchResults search(final String searchString, final int maxHits) thr
             return new PdfSearchResults();
         }
         try (IndexReader reader = DirectoryReader.open(optionalIndexWriter.get())) {
-            Query query = new MultiFieldQueryParser(PDF_FIELDS, englishStemAnalyzer).parse(searchString);
+            Query query = new MultiFieldQueryParser(PDF_FIELDS, englishAnalyzer).parse(searchString);
             IndexSearcher searcher = new IndexSearcher(reader);
             TopDocs results = searcher.search(query, maxHits);
             for (ScoreDoc scoreDoc : results.scoreDocs) {
diff --git a/src/main/java/org/jabref/model/pdf/search/EnglishStemAnalyzer.java b/src/main/java/org/jabref/model/pdf/search/EnglishStemAnalyzer.java
deleted file mode 100644
index 1dcccbb6583..00000000000
--- a/src/main/java/org/jabref/model/pdf/search/EnglishStemAnalyzer.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package org.jabref.model.pdf.search;
-
-import org.apache.lucene.analysis.Analyzer;
-import org.apache.lucene.analysis.LowerCaseFilter;
-import org.apache.lucene.analysis.StopFilter;
-import org.apache.lucene.analysis.TokenStream;
-import org.apache.lucene.analysis.Tokenizer;
-import org.apache.lucene.analysis.core.DecimalDigitFilter;
-import org.apache.lucene.analysis.en.EnglishAnalyzer;
-import org.apache.lucene.analysis.en.PorterStemFilter;
-import org.apache.lucene.analysis.standard.StandardTokenizer;
-
-public class EnglishStemAnalyzer extends Analyzer {
-
-    @Override
-    protected TokenStreamComponents createComponents(String fieldName) {
-        Tokenizer source = new StandardTokenizer();
-        TokenStream filter = new LowerCaseFilter(source);
-        filter = new StopFilter(filter, EnglishAnalyzer.ENGLISH_STOP_WORDS_SET);
-        filter = new DecimalDigitFilter(filter);
-        filter = new PorterStemFilter(filter);
-        return new TokenStreamComponents(source, filter);
-    }
-}
-
diff --git a/src/main/java/org/jabref/model/pdf/search/SearchResult.java b/src/main/java/org/jabref/model/pdf/search/SearchResult.java
index 7a79191e94c..aeb70ff6779 100644
--- a/src/main/java/org/jabref/model/pdf/search/SearchResult.java
+++ b/src/main/java/org/jabref/model/pdf/search/SearchResult.java
@@ -7,7 +7,9 @@
 
 import org.jabref.model.entry.BibEntry;
 
+import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.analysis.TokenStream;
+import org.apache.lucene.analysis.en.EnglishAnalyzer;
 import org.apache.lucene.index.IndexableField;
 import org.apache.lucene.search.IndexSearcher;
 import org.apache.lucene.search.Query;
@@ -46,14 +48,16 @@ public SearchResult(IndexSearcher searcher, Query query, ScoreDoc scoreDoc) thro
 
         Highlighter highlighter = new Highlighter(new SimpleHTMLFormatter("<b>", "</b>"), new QueryScorer(query));
 
-        try (TokenStream contentStream = new EnglishStemAnalyzer().tokenStream(CONTENT, content)) {
+        try (Analyzer analyzer = new EnglishAnalyzer();
+             TokenStream contentStream = analyzer.tokenStream(CONTENT, content)) {
             TextFragment[] frags = highlighter.getBestTextFragments(contentStream, content, true, 10);
             this.contentResultStringsHtml = Arrays.stream(frags).map(TextFragment::toString).collect(Collectors.toList());
         } catch (InvalidTokenOffsetsException e) {
             this.contentResultStringsHtml = List.of();
         }
 
-        try (TokenStream annotationStream = new EnglishStemAnalyzer().tokenStream(ANNOTATIONS, annotations)) {
+        try (Analyzer analyzer = new EnglishAnalyzer();
+             TokenStream annotationStream = analyzer.tokenStream(ANNOTATIONS, annotations)) {
             TextFragment[] frags = highlighter.getBestTextFragments(annotationStream, annotations, true, 10);
             this.annotationsResultStringsHtml = Arrays.stream(frags).map(TextFragment::toString).collect(Collectors.toList());
         } catch (InvalidTokenOffsetsException e) {
@@ -62,7 +66,7 @@ public SearchResult(IndexSearcher searcher, Query query, ScoreDoc scoreDoc) thro
     }
 
     private String getFieldContents(IndexSearcher searcher, ScoreDoc scoreDoc, String field) throws IOException {
-        IndexableField indexableField = searcher.doc(scoreDoc.doc).getField(field);
+        IndexableField indexableField = searcher.storedFields().document(scoreDoc.doc).getField(field);
         if (indexableField == null) {
             return "";
         }

From dfe1b0ce0bbd185ed5747b70e7ca24e4f05ebf37 Mon Sep 17 00:00:00 2001
From: Loay Ghreeb <52158423+LoayGhreeb@users.noreply.github.com>
Date: Sat, 18 May 2024 21:47:55 +0300
Subject: [PATCH 54/54] Update latex citations status in JavaFx thread (#11302)

* Update status in JavaFx thread

* Update LatexCitationsTabViewModel.java
---
 .../org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
index 2549e9ec211..7f6d74cc94f 100644
--- a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
@@ -92,7 +92,7 @@ private FileAlterationListener getListener() {
             @Override
             public void onStart(FileAlterationObserver observer) {
                 if (!updateStatusOnCreate.get()) {
-                    status.set(Status.IN_PROGRESS);
+                    DefaultTaskExecutor.runInJavaFXThread(() -> status.set(Status.IN_PROGRESS));
                 }
             }