From 1114a98a8a169e4018cd113641d30b728fb4171f Mon Sep 17 00:00:00 2001
From: Joan Viladrosa <joan@moderne.io>
Date: Tue, 5 Sep 2023 00:17:34 +0200
Subject: [PATCH 01/20] fixed project provenance on gradle files (#226)

---
 .../gradle/isolated/DefaultProjectParser.java | 35 +++++++++++--------
 1 file changed, 21 insertions(+), 14 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 4ae1ebc87..16d19d843 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -640,7 +640,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
             if (subproject.getPlugins().hasPlugin("org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformExtension") ||
                 subproject.getExtensions().findByName("kotlin") != null && subproject.getExtensions().getByName("kotlin").getClass()
                         .getCanonicalName().startsWith("org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformExtension")) {
-                sourceFileStream = sourceFileStream.concat(parseMultiplatformKotlinProject(subproject, exclusions, alreadyParsed, projectProvenance, ctx));
+                sourceFileStream = sourceFileStream.concat(parseMultiplatformKotlinProject(subproject, exclusions, alreadyParsed, ctx));
             }
 
             for (SourceSet sourceSet : sourceSets) {
@@ -798,17 +798,18 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 JavaSourceSet sourceSetProvenance = JavaSourceSet.build(sourceSet.getName(), dependencyPaths, javaTypeCache, false);
-                sourceFileStream = sourceFileStream.concat(sourceSetSourceFiles.map(addProvenance(projectProvenance, sourceSetProvenance)), sourceSetSize);
+                sourceFileStream = sourceFileStream.concat(sourceSetSourceFiles.map(addProvenance(sourceSetProvenance)), sourceSetSize);
             }
-
-            sourceFileStream = sourceFileStream.concat(parseGradleFiles(exclusions, alreadyParsed, ctx));
+            SourceFileStream gradleFiles = parseGradleFiles(exclusions, alreadyParsed, ctx);
+            sourceFileStream = sourceFileStream.concat(gradleFiles, gradleFiles.size());
 
             SourceFileStream nonProjectResources = parseNonProjectResources(subproject, alreadyParsed, ctx, projectProvenance, sourceFileStream);
-            sourceFileStream = sourceFileStream.concat(nonProjectResources
-                    .map(addProvenance(projectProvenance, null)), nonProjectResources.size());
+            sourceFileStream = sourceFileStream.concat(nonProjectResources, nonProjectResources.size());
 
             progressBar.setMax(sourceFileStream.size());
-            return sourceFileStream.peek(it -> progressBar.step());
+            return sourceFileStream
+                    .map(addProvenance(projectProvenance))
+                    .peek(it -> progressBar.step());
         } catch (Exception e) {
             throw new RuntimeException(e);
         }
@@ -952,7 +953,7 @@ private Collection<PathMatcher> pathMatchers(Path basePath, Collection<String> p
                 .collect(Collectors.toList());
     }
 
-    private SourceFileStream parseMultiplatformKotlinProject(Project subproject, Collection<PathMatcher> exclusions, Set<Path> alreadyParsed, List<Marker> projectProvenance, ExecutionContext ctx) {
+    private SourceFileStream parseMultiplatformKotlinProject(Project subproject, Collection<PathMatcher> exclusions, Set<Path> alreadyParsed, ExecutionContext ctx) {
         Object kotlinExtension = subproject.getExtensions().getByName("kotlin");
         NamedDomainObjectContainer<KotlinSourceSet> sourceSets;
         try {
@@ -1044,7 +1045,7 @@ private SourceFileStream parseMultiplatformKotlinProject(Project subproject, Col
                     }).filter(Objects::nonNull);
                     JavaSourceSet sourceSetProvenance = JavaSourceSet.build(sourceSetName, dependencyPaths, javaTypeCache, false);
 
-                    sourceFileStream = sourceFileStream.concat(cus.map(addProvenance(projectProvenance, sourceSetProvenance)), kotlinPaths.size());
+                    sourceFileStream = sourceFileStream.concat(cus.map(addProvenance(sourceSetProvenance)), kotlinPaths.size());
                     logger.info("Scanned {} Kotlin sources in {}/{}", kotlinPaths.size(), subproject.getPath(), kotlinDirectorySet.getName());
                 }
                 return sourceFileStream;
@@ -1150,19 +1151,25 @@ private UnaryOperator<SourceFile> applyAutodetectedStyle(Map<Class<? extends Tre
         };
     }
 
-    private <T extends SourceFile> UnaryOperator<T> addProvenance(List<Marker> projectProvenance, @Nullable Marker sourceSet) {
+    private <T extends SourceFile> UnaryOperator<T> addProvenance(List<Marker> projectProvenance) {
         return s -> {
             Markers m = s.getMarkers();
             for (Marker marker : projectProvenance) {
-                m = m.add(marker);
-            }
-            if (sourceSet != null) {
-                m = m.add(sourceSet);
+                m = m.addIfAbsent(marker);
             }
             return s.withMarkers(m);
         };
     }
 
+    private <T extends SourceFile> UnaryOperator<T> addProvenance(Marker sourceSet) {
+        return s -> {
+            Markers m = s.getMarkers();
+            m = m.addIfAbsent(sourceSet);
+            return s.withMarkers(m);
+        };
+    }
+
+
     protected void logRecipesThatMadeChanges(Result result) {
         String indent = "    ";
         String prefix = "    ";

From 5927ee44626e7dbfebbcb9596d089b5eeda0aba2 Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Thu, 7 Sep 2023 20:38:12 -0700
Subject: [PATCH 02/20] Don't double-parse files that appear in multiple,
 overlapping source sets

---
 plugin/build.gradle.kts                       |  5 +-
 .../org/openrewrite/gradle/RewritePlugin.java | 34 +++++++-
 .../gradle/isolated/DefaultProjectParser.java | 31 ++++++--
 .../org/openrewrite/gradle/RewriteRunTest.kt  | 77 +++++++++++++++++++
 4 files changed, 134 insertions(+), 13 deletions(-)

diff --git a/plugin/build.gradle.kts b/plugin/build.gradle.kts
index 194c0a184..003ddf497 100644
--- a/plugin/build.gradle.kts
+++ b/plugin/build.gradle.kts
@@ -67,7 +67,6 @@ configurations.all {
     }
 }
 
-
 java {
     toolchain {
         languageVersion.set(JavaLanguageVersion.of(17))
@@ -109,6 +108,7 @@ dependencies {
     "rewriteDependencies"("org.openrewrite.gradle.tooling:model:$latest")
     "rewriteDependencies"("org.openrewrite:rewrite-maven")
     // Newer versions of checkstyle are compiled with a newer version of Java than is supported with gradle 4.x
+    @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     "rewriteDependencies"("com.puppycrawl.tools:checkstyle:9.3")
     "rewriteDependencies"("com.fasterxml.jackson.module:jackson-module-kotlin:latest.release")
 
@@ -126,6 +126,7 @@ dependencies {
     compileOnly("org.openrewrite:rewrite-xml")
     compileOnly("org.openrewrite:rewrite-yaml")
     compileOnly("org.openrewrite:rewrite-polyglot:$latest")
+    @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     compileOnly("com.puppycrawl.tools:checkstyle:9.3")
     compileOnly("org.jetbrains.kotlin:kotlin-gradle-plugin:latest.release")
 
@@ -155,7 +156,7 @@ tasks.withType<Test>() {
 }
 
 val gVP = tasks.register("generateVersionsProperties") {
-    val outputFile = file("$buildDir/rewrite/versions.properties")
+    val outputFile = file("${project.layout.buildDirectory.get().asFile}/rewrite/versions.properties")
     description = "Creates a versions.properties in $outputFile"
     group = "Build"
 
diff --git a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
index 8949fe13f..1549446dd 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
@@ -22,6 +22,11 @@
 import org.gradle.api.plugins.quality.CheckstyleExtension;
 import org.gradle.api.plugins.quality.CheckstylePlugin;
 
+import java.io.File;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * When applied to the root project of a multi-project build, applies to all subprojects.
  * When applied to the root project the "rewrite" configuration and "rewrite" DSL created in the root project apply to
@@ -37,7 +42,7 @@ public void apply(Project project) {
         if (!isRootProject && project.getRootProject().getPluginManager().hasPlugin("org.openrewrite.rewrite")) {
             return;
         }
-        if(project.getRootProject().getPluginManager().hasPlugin("io.moderne.rewrite")) {
+        if (project.getRootProject().getPluginManager().hasPlugin("io.moderne.rewrite")) {
             // Moderne plugin provides superset of rewrite plugin functionality, no need to apply both
             return;
         }
@@ -67,7 +72,7 @@ public void apply(Project project) {
                 .setResolveDependenciesTask(resolveRewriteDependenciesTask);
         rewriteDiscover.dependsOn(rewriteConf);
 
-        if(isRootProject) {
+        if (isRootProject) {
             project.allprojects(subproject -> configureProject(subproject, extension, rewriteDryRun, rewriteRun));
         } else {
             configureProject(project, extension, rewriteDryRun, rewriteRun);
@@ -78,14 +83,14 @@ private static void configureProject(Project project, RewriteExtension extension
         // DomainObjectCollection.all() accepts a function to be applied to both existing and subsequently added members of the collection
         // Do not replace all() with any form of collection iteration which does not share this important property
         project.getPlugins().all(plugin -> {
-            if(plugin instanceof CheckstylePlugin) {
+            if (plugin instanceof CheckstylePlugin) {
                 // A multi-project build could hypothetically have different checkstyle configuration per-project
                 // In practice all projects tend to have the same configuration
                 CheckstyleExtension checkstyleExtension = project.getExtensions().getByType(CheckstyleExtension.class);
                 extension.setCheckstyleConfigProvider(checkstyleExtension::getConfigFile);
                 extension.setCheckstylePropertiesProvider(checkstyleExtension::getConfigProperties);
             }
-            if(!(plugin instanceof JavaBasePlugin)) {
+            if (!(plugin instanceof JavaBasePlugin)) {
                 return;
             }
 
@@ -99,6 +104,27 @@ private static void configureProject(Project project, RewriteExtension extension
                 rewriteRun.dependsOn(compileTask);
                 rewriteDryRun.dependsOn(compileTask);
             });
+
+            // Detect SourceSets which overlap other sourceSets and disable the compilation task of the overlapping
+            // source set. Some plugins will create source sets not intended to be compiled for their own purposes.
+            Set<String> sourceDirs = new HashSet<>();
+            project.afterEvaluate(unused -> javaConvention.getSourceSets().stream()
+                    .sorted(Comparator.comparingInt(sourceSet -> {
+                        if ("main".equals(sourceSet.getName())) {
+                            return 0;
+                        } else if ("test".equals(sourceSet.getName())) {
+                            return 1;
+                        } else {
+                            return 2;
+                        }
+                    })).forEach(sourceSet -> {
+                        for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                            if (!sourceDirs.add(file.getAbsolutePath())) {
+                                Task compileTask = project.getTasks().getByPath(sourceSet.getCompileJavaTaskName());
+                                compileTask.setEnabled(false);
+                            }
+                        }
+                    }));
         });
     }
 }
diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 16d19d843..fd1ee6f1d 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -85,7 +85,6 @@
 import java.util.function.Consumer;
 import java.util.function.Supplier;
 import java.util.function.UnaryOperator;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import static java.util.Collections.*;
@@ -119,7 +118,7 @@ public DefaultProjectParser(Project project, RewriteExtension extension) {
                         OperatingSystemProvenance.current(),
                         new BuildTool(randomId(), BuildTool.Type.Gradle, project.getGradle().getGradleVersion()))
                 .filter(Objects::nonNull)
-                .collect(Collectors.toList());
+                .collect(toList());
     }
 
     /**
@@ -185,7 +184,7 @@ public List<String> getActiveStyles() {
     }
 
     public List<String> getAvailableStyles() {
-        return environment().listStyles().stream().map(NamedStyles::getName).collect(Collectors.toList());
+        return environment().listStyles().stream().map(NamedStyles::getName).collect(toList());
     }
 
     public void discoverRecipes(boolean interactive, ServiceRegistry serviceRegistry) {
@@ -623,18 +622,27 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
             List<NamedStyles> styles = getStyles();
             @SuppressWarnings("deprecation")
             JavaPluginConvention javaConvention = subproject.getConvention().findPlugin(JavaPluginConvention.class);
-            Set<SourceSet> sourceSets;
+            List<SourceSet> sourceSets;
             List<Marker> projectProvenance;
             if (javaConvention == null) {
                 projectProvenance = sharedProvenance;
-                sourceSets = Collections.emptySet();
+                sourceSets = emptyList();
             } else {
                 projectProvenance = new ArrayList<>(sharedProvenance);
                 projectProvenance.add(new JavaProject(randomId(), subproject.getName(),
                         new JavaProject.Publication(subproject.getGroup().toString(),
                                 subproject.getName(),
                                 subproject.getVersion().toString())));
-                sourceSets = javaConvention.getSourceSets();
+                sourceSets = javaConvention.getSourceSets().stream()
+                        .sorted(Comparator.comparingInt(sourceSet -> {
+                            if ("main".equals(sourceSet.getName())) {
+                                return 0;
+                            } else if ("test".equals(sourceSet.getName())) {
+                                return 1;
+                            } else {
+                                return 2;
+                            }
+                        })).collect(toList());
             }
 
             if (subproject.getPlugins().hasPlugin("org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformExtension") ||
@@ -643,7 +651,16 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 sourceFileStream = sourceFileStream.concat(parseMultiplatformKotlinProject(subproject, exclusions, alreadyParsed, ctx));
             }
 
+            Set<String> sourceDirs = new HashSet<>();
+            sourceSetLoop:
             for (SourceSet sourceSet : sourceSets) {
+                        // Detect SourceSets which overlap other sourceSets and disable the compilation task of the overlapping
+            // source set. Skip parsing directories already covered by another source set.
+                for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                    if (!sourceDirs.add(file.getAbsolutePath())) {
+                        continue sourceSetLoop;
+                    }
+                }
                 Stream<SourceFile> sourceSetSourceFiles = Stream.of();
                 int sourceSetSize = 0;
 
@@ -950,7 +967,7 @@ private static Collection<String> mergeExclusions(Project project, Path baseDir,
     private Collection<PathMatcher> pathMatchers(Path basePath, Collection<String> pathExpressions) {
         return pathExpressions.stream()
                 .map(o -> basePath.getFileSystem().getPathMatcher("glob:" + o))
-                .collect(Collectors.toList());
+                .collect(toList());
     }
 
     private SourceFileStream parseMultiplatformKotlinProject(Project subproject, Collection<PathMatcher> exclusions, Set<Path> alreadyParsed, ExecutionContext ctx) {
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index a86891f7d..41cd37646 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -972,4 +972,81 @@ class RewriteRunTest : RewritePluginTest {
             .`as`("Applicability test should have prevented this file from being altered")
             .isEqualTo("jonathan")
     }
+
+    @Test
+    fun overlappingSourceSet(@TempDir buildRoot: File) {
+        gradleProject(buildRoot) {
+            rewriteYaml("""
+              type: specs.openrewrite.org/v1beta/recipe
+              name: org.openrewrite.test.FindSneaky
+              displayName: Find lombok SneakyThrows annotation
+              description: Find lombok SneakyThrows annotation
+              recipeList:
+                - org.openrewrite.java.search.FindTypes:
+                    fullyQualifiedTypeName: lombok.SneakyThrows
+            """)
+            buildGradle("""
+                plugins { 
+                    id("java")
+                    id("org.openrewrite.rewrite")
+                }
+                
+                repositories {
+                    mavenLocal()
+                    mavenCentral()
+                    maven {
+                       url = uri("https://oss.sonatype.org/content/repositories/snapshots")
+                    }
+                }
+                
+                sourceSets {
+                    create("overlapping") {
+                        java.srcDir("src/test/java")
+                    }
+                }
+                
+                rewrite {
+                    activeRecipe("org.openrewrite.test.FindSneaky")
+                }
+                
+                dependencies {
+                    testImplementation("org.projectlombok:lombok:latest.release")
+                }
+            """)
+            sourceSet("test") {
+                java("""
+                    package com.foo;
+                    
+                    import lombok.SneakyThrows;
+                    
+                    public class ATest {
+                    
+                        @SneakyThrows
+                        public void fail() { 
+                        }
+                    }
+                """)
+            }
+        }
+
+        val result = runGradle(buildRoot, "rewriteRun")
+        val rewriteRunResult = result.task(":rewriteRun")!!
+        assertThat(rewriteRunResult.outcome).isEqualTo(TaskOutcome.SUCCESS)
+        val javaFile = buildRoot.resolve("src/test/java/com/foo/ATest.java")
+        assertThat(javaFile.readText())
+            //language=java
+            .isEqualTo("""
+                package com.foo;
+                
+                import lombok.SneakyThrows;
+                
+                public class ATest {
+                
+                    @/*~~>*/SneakyThrows
+                    public void fail() { 
+                    }
+                }
+                """.trimIndent()
+            )
+    }
 }

From 903faa813c8061f2ac97f72b430f22ccf0e42122 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Sep 2023 17:26:44 +0100
Subject: [PATCH 03/20] chore(ci): bump actions/checkout from 3.6.0 to 4 (#229)

* chore(ci): bump actions/checkout from 3.6.0 to 4.0.0

Bumps [actions/checkout](https://github.com/actions/checkout) from 3.6.0 to 4.0.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3.6.0...v4.0.0)

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

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

* Apply suggestions from code review

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tim te Beek <tim@moderne.io>
---
 .github/workflows/ci.yml                | 2 +-
 .github/workflows/integration-tests.yml | 4 ++--
 .github/workflows/publish.yml           | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 83d0bfede..234b3d021 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-java@v3
diff --git a/.github/workflows/integration-tests.yml b/.github/workflows/integration-tests.yml
index 5d53aaeed..323cefe4e 100644
--- a/.github/workflows/integration-tests.yml
+++ b/.github/workflows/integration-tests.yml
@@ -20,11 +20,11 @@ jobs:
     name: itest-${{ matrix.java }}
     steps:
       - name: checkout-openrewrite/spring-petclinic-migration
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4
         with:
           repository: openrewrite/spring-petclinic-migration
       - name: setup-plugin-checkout-source
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4
         with:
           path: rewrite-gradle-plugin
       - name: setup-plugin-setup-java-11
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 72f71d683..5c243aedb 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -16,7 +16,7 @@ jobs:
   release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-java@v3

From ce73e203a0be839191635063b4f4e15fba69fc34 Mon Sep 17 00:00:00 2001
From: Knut Wannheden <knut@moderne.io>
Date: Fri, 22 Sep 2023 23:33:10 +0200
Subject: [PATCH 04/20] Makes sure `.kt` sources are contained in
 `listSources()` (#225)

---
 .../org/openrewrite/gradle/isolated/DefaultProjectParser.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index fd1ee6f1d..8afe696f9 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -273,7 +273,7 @@ public Collection<Path> listSources() {
         JavaPluginConvention javaConvention = project.getConvention().findPlugin(JavaPluginConvention.class);
         if (javaConvention != null) {
             for (SourceSet sourceSet : javaConvention.getSourceSets()) {
-                sourceSet.getAllJava().getFiles().stream()
+                sourceSet.getAllSource().getFiles().stream()
                         .filter(it -> it.isFile() && (it.getName().endsWith(".java") || it.getName().endsWith(".kt")))
                         .map(File::toPath)
                         .map(Path::toAbsolutePath)

From 2553b5485bb82a7fd03a427902e85527c177f6ef Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 22 Sep 2023 17:26:43 -0700
Subject: [PATCH 05/20] Fix #231 non-source code files in subprojects parsed
 multiple times with incorrect paths

---
 .../gradle/isolated/DefaultProjectParser.java | 25 +++++++++++--------
 .../org/openrewrite/gradle/RewriteRunTest.kt  | 21 +++++++++++++---
 2 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 8afe696f9..0442d6566 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -268,7 +268,7 @@ private static StringBuilder repeat(int repeat) {
 
     public Collection<Path> listSources() {
         // Use a sorted collection so that gradle input detection isn't thrown off by ordering
-        Set<Path> result = new TreeSet<>(omniParser(emptySet()).acceptedPaths(project.getProjectDir().toPath()));
+        Set<Path> result = new TreeSet<>(omniParser(emptySet()).build().acceptedPaths(baseDir, project.getProjectDir().toPath()));
         //noinspection deprecation
         JavaPluginConvention javaConvention = project.getConvention().findPlugin(JavaPluginConvention.class);
         if (javaConvention != null) {
@@ -292,6 +292,7 @@ public void dryRun(Path reportPath, boolean dumpGcActivity, Consumer<Throwable>
                 heapMetrics.bindTo(meterRegistry);
                 new JvmMemoryMetrics().bindTo(meterRegistry);
 
+                //noinspection deprecation
                 File rewriteBuildDir = new File(project.getBuildDir(), "/rewrite");
                 if (rewriteBuildDir.exists() || rewriteBuildDir.mkdirs()) {
                     File rewriteGcLog = new File(rewriteBuildDir, "rewrite-gc.csv");
@@ -715,6 +716,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                             .map(Supplier::get)
                             .flatMap(jp -> jp.parse(javaPaths, baseDir, ctx))
                             .map(cu -> {
+                                //noinspection deprecation
                                 if (isExcluded(exclusions, cu.getSourcePath()) ||
                                     cu.getSourcePath().startsWith(baseDir.relativize(subproject.getBuildDir().toPath()))) {
                                     return null;
@@ -804,12 +806,13 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
                     if (resourcesDir.exists()) {
-                        OmniParser omniParser = omniParser(alreadyParsed);
-                        List<Path> accepted = omniParser.acceptedPaths(resourcesDir.toPath());
+                        OmniParser omniParser = omniParser(alreadyParsed).build();
+                        List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
                                 sourceSetSourceFiles,
-                                omniParser.parse(accepted, resourcesDir.toPath(), new InMemoryExecutionContext())
+                                omniParser.parse(accepted, baseDir, new InMemoryExecutionContext())
                         );
+                        alreadyParsed.addAll(accepted);
                         sourceSetSize += accepted.size();
                     }
                 }
@@ -936,13 +939,14 @@ private SourceFileStream parseGradleFiles(
 
     protected SourceFileStream parseNonProjectResources(Project subproject, Set<Path> alreadyParsed, ExecutionContext ctx, List<Marker> projectProvenance, Stream<SourceFile> sourceFiles) {
         //Collect any additional yaml/properties/xml files that are NOT already in a source set.
-        OmniParser omniParser = omniParser(alreadyParsed);
-        List<Path> accepted = omniParser.acceptedPaths(subproject.getProjectDir().toPath());
-        return SourceFileStream.build("", s -> {
-        }).concat(omniParser.parse(accepted, subproject.getProjectDir().toPath(), ctx), accepted.size());
+        OmniParser omniParser = omniParser(alreadyParsed)
+                .build();
+        List<Path> accepted = omniParser.acceptedPaths(baseDir, subproject.getProjectDir().toPath());
+        return SourceFileStream.build("", s -> {})
+                .concat(omniParser.parse(accepted, baseDir, ctx), accepted.size());
     }
 
-    private OmniParser omniParser(Set<Path> alreadyParsed) {
+    private OmniParser.Builder omniParser(Set<Path> alreadyParsed) {
         return OmniParser.builder(
                         OmniParser.RESOURCE_PARSERS,
                         PlainTextParser.builder()
@@ -952,8 +956,7 @@ private OmniParser omniParser(Set<Path> alreadyParsed) {
                 )
                 .exclusionMatchers(pathMatchers(baseDir, mergeExclusions(project, baseDir, extension)))
                 .exclusions(alreadyParsed)
-                .sizeThresholdMb(extension.getSizeThresholdMb())
-                .build();
+                .sizeThresholdMb(extension.getSizeThresholdMb());
     }
 
     private static Collection<String> mergeExclusions(Project project, Path baseDir, RewriteExtension extension) {
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index 41cd37646..fd3052a85 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -156,12 +156,12 @@ class RewriteRunTest : RewritePluginTest {
     }
 
     @Test
-    fun `rewriteRun applies built-in AutoFormat to a multi-project build`(
+    fun `rewriteRun applies recipe to a multi-project build`(
         @TempDir projectDir: File
     ) {
         val bTestClassExpected = """
                 package com.foo;
-    
+                
                 import org.junit.Test;
                 
                 public class BTestClass {
@@ -171,6 +171,15 @@ class RewriteRunTest : RewritePluginTest {
                 }
         """.trimIndent()
         gradleProject(projectDir) {
+            rewriteYaml("""
+                type: specs.openrewrite.org/v1beta/recipe
+                name: org.openrewrite.FormatAndAddProperty
+                recipeList:
+                  - org.openrewrite.java.format.AutoFormat
+                  - org.openrewrite.properties.ChangePropertyKey:
+                      oldPropertyKey: foo
+                      newPropertyKey: bar
+            """)
             buildGradle("""
                 plugins {
                     id("org.openrewrite.rewrite")
@@ -178,7 +187,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
                 rewrite {
-                    activeRecipe("org.openrewrite.java.format.AutoFormat")
+                    activeRecipe("org.openrewrite.FormatAndAddProperty")
                     exclusion("**/BTestClass.java")
                 }
                 
@@ -216,6 +225,7 @@ class RewriteRunTest : RewritePluginTest {
                             public void passes() { }
                         }
                     """)
+                    propertiesFile("test.properties", "foo=baz\n")
                 }
             }
             subproject("b") {
@@ -231,7 +241,7 @@ class RewriteRunTest : RewritePluginTest {
         //language=java
         val aTestClassExpected = """
             package com.foo;
-
+            
             import org.junit.Test;
             
             public class ATestClass {
@@ -245,6 +255,9 @@ class RewriteRunTest : RewritePluginTest {
         assertThat(aTestClassFile.readText()).isEqualTo(aTestClassExpected)
         val bTestClassFile = File(projectDir, "b/src/test/java/com/foo/BTestClass.java")
         assertThat(bTestClassFile.readText()).isEqualTo(bTestClassExpected)
+
+        val propertiesFile = File(projectDir, "a/src/test/resources/test.properties")
+        assertThat(propertiesFile.readText()).isEqualTo("bar=baz\n")
     }
 
     @Suppress("ClassInitializerMayBeStatic", "StatementWithEmptyBody", "ConstantConditions")

From da10e291edc2c4b0edc3a0ebad8e5e1ff7be7ddf Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 22 Sep 2023 17:29:07 -0700
Subject: [PATCH 06/20] Polish

---
 .../gradle/isolated/DefaultProjectParser.java        | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 0442d6566..2656bd9cf 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -268,7 +268,7 @@ private static StringBuilder repeat(int repeat) {
 
     public Collection<Path> listSources() {
         // Use a sorted collection so that gradle input detection isn't thrown off by ordering
-        Set<Path> result = new TreeSet<>(omniParser(emptySet()).build().acceptedPaths(baseDir, project.getProjectDir().toPath()));
+        Set<Path> result = new TreeSet<>(omniParser(emptySet()).acceptedPaths(baseDir, project.getProjectDir().toPath()));
         //noinspection deprecation
         JavaPluginConvention javaConvention = project.getConvention().findPlugin(JavaPluginConvention.class);
         if (javaConvention != null) {
@@ -806,7 +806,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
                     if (resourcesDir.exists()) {
-                        OmniParser omniParser = omniParser(alreadyParsed).build();
+                        OmniParser omniParser = omniParser(alreadyParsed);
                         List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
                                 sourceSetSourceFiles,
@@ -939,14 +939,13 @@ private SourceFileStream parseGradleFiles(
 
     protected SourceFileStream parseNonProjectResources(Project subproject, Set<Path> alreadyParsed, ExecutionContext ctx, List<Marker> projectProvenance, Stream<SourceFile> sourceFiles) {
         //Collect any additional yaml/properties/xml files that are NOT already in a source set.
-        OmniParser omniParser = omniParser(alreadyParsed)
-                .build();
+        OmniParser omniParser = omniParser(alreadyParsed);
         List<Path> accepted = omniParser.acceptedPaths(baseDir, subproject.getProjectDir().toPath());
         return SourceFileStream.build("", s -> {})
                 .concat(omniParser.parse(accepted, baseDir, ctx), accepted.size());
     }
 
-    private OmniParser.Builder omniParser(Set<Path> alreadyParsed) {
+    private OmniParser omniParser(Set<Path> alreadyParsed) {
         return OmniParser.builder(
                         OmniParser.RESOURCE_PARSERS,
                         PlainTextParser.builder()
@@ -956,7 +955,8 @@ private OmniParser.Builder omniParser(Set<Path> alreadyParsed) {
                 )
                 .exclusionMatchers(pathMatchers(baseDir, mergeExclusions(project, baseDir, extension)))
                 .exclusions(alreadyParsed)
-                .sizeThresholdMb(extension.getSizeThresholdMb());
+                .sizeThresholdMb(extension.getSizeThresholdMb())
+                .build();
     }
 
     private static Collection<String> mergeExclusions(Project project, Path baseDir, RewriteExtension extension) {

From 3975972d2a7b682d59d6f70e742d6e4feaa24ba4 Mon Sep 17 00:00:00 2001
From: Jonathan Schneider <jkschneider@gmail.com>
Date: Sun, 24 Sep 2023 02:18:34 -0400
Subject: [PATCH 07/20] RESOURCE_PARSERS -> defaultResourceParsers()

---
 .../org/openrewrite/gradle/isolated/DefaultProjectParser.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 2656bd9cf..bc8d72ce9 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -947,7 +947,7 @@ protected SourceFileStream parseNonProjectResources(Project subproject, Set<Path
 
     private OmniParser omniParser(Set<Path> alreadyParsed) {
         return OmniParser.builder(
-                        OmniParser.RESOURCE_PARSERS,
+                        OmniParser.defaultResourceParsers(),
                         PlainTextParser.builder()
                                 .plainTextMasks(baseDir, extension.getPlainTextMasks())
                                 .build(),

From 01707ca029b8d1f156a492d2cbc4ac7d2ba46466 Mon Sep 17 00:00:00 2001
From: Tim te Beek <tim@moderne.io>
Date: Mon, 25 Sep 2023 11:38:38 +0200
Subject: [PATCH 08/20] Jenkinsfiles now parsed as Groovy

---
 .../java/org/openrewrite/gradle/DefaultRewriteExtension.java     | 1 -
 1 file changed, 1 deletion(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
index 2208aa03c..5f31d93b4 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
@@ -343,7 +343,6 @@ public List<String> getPlainTextMasks() {
                     "**.gitattributes",
                     "**.gitignore",
                     "**.java-version",
-                    "**Jenkinsfile",
                     "**.jsp",
                     "**.ksh",
                     "**.kts",

From e34bcf0b80ddd132eaae4218a5bd6bd93be7a516 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jonathan=20Schn=C3=A9ider?= <jkschneider@gmail.com>
Date: Tue, 26 Sep 2023 18:47:13 +0000
Subject: [PATCH 09/20] refactor: Spaces

Use this link to re-run the recipe: https://app.moderne.io/recipes/org.openrewrite.java.format.Spaces?organizationId=T3BlblJld3JpdGU%3D

Co-authored-by: Moderne <team@moderne.io>
---
 .../gradle/AbstractRewriteTask.java           |  4 +-
 .../gradle/DefaultRewriteExtension.java       | 24 +++---
 .../gradle/DelegatingProjectParser.java       |  2 +-
 .../gradle/SanitizedMarkerPrinter.java        |  4 +-
 .../org/openrewrite/gradle/TimeUtils.java     | 18 ++---
 .../openrewrite/gradle/GradleProjectSpec.kt   | 62 +++++++-------
 .../openrewrite/gradle/RewriteDiscoverTest.kt |  2 +-
 .../openrewrite/gradle/RewriteDryRunTest.kt   | 12 +--
 .../openrewrite/gradle/RewritePluginTest.kt   |  2 +-
 .../org/openrewrite/gradle/RewriteRunTest.kt  | 80 +++++++++----------
 scripts/spring-petclinic-test.init.gradle     | 38 ++++-----
 11 files changed, 124 insertions(+), 124 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/AbstractRewriteTask.java b/plugin/src/main/java/org/openrewrite/gradle/AbstractRewriteTask.java
index 8ac585073..ddecf1501 100755
--- a/plugin/src/main/java/org/openrewrite/gradle/AbstractRewriteTask.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/AbstractRewriteTask.java
@@ -57,8 +57,8 @@ public boolean isDumpGcActivity() {
 
     @Internal
     protected <T extends GradleProjectParser> T getProjectParser() {
-        if(gpp == null) {
-            if(extension == null) {
+        if (gpp == null) {
+            if (extension == null) {
                 throw new IllegalArgumentException("Must configure extension");
             }
             if (resolveDependenciesTask == null) {
diff --git a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
index 5f31d93b4..a8856d872 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
@@ -38,7 +38,7 @@ public class DefaultRewriteExtension implements RewriteExtension {
     private File configFile;
 
     private Provider<File> checkstyleConfigProvider;
-    private Provider<Map<String,Object>> checkstylePropertiesProvider;
+    private Provider<Map<String, Object>> checkstylePropertiesProvider;
     private File checkstyleConfigFile;
     private String metricsUri = magicalMetricsLogString;
     private boolean enableExperimentalGradleBuildScriptParsing = true;
@@ -98,10 +98,10 @@ public void setCheckstyleConfigFile(File configFile) {
     @Override
     @Nullable
     public File getCheckstyleConfigFile() {
-        if(checkstyleConfigFile == null && checkstyleConfigProvider != null) {
+        if (checkstyleConfigFile == null && checkstyleConfigProvider != null) {
             try {
                 return checkstyleConfigProvider.get();
-            } catch(Exception e) {
+            } catch (Exception e) {
                 return null;
             }
         }
@@ -110,7 +110,7 @@ public File getCheckstyleConfigFile() {
 
     @Override
     public Map<String, Object> getCheckstyleProperties() {
-        if(checkstyleConfigProvider == null) {
+        if (checkstyleConfigProvider == null) {
             return emptyMap();
         }
         return checkstylePropertiesProvider.get();
@@ -195,11 +195,11 @@ public List<String> getActiveRecipes() {
     }
 
     private Properties getVersionProps() {
-        if(versionProps == null) {
-            try(InputStream is = DefaultRewriteExtension.class.getResourceAsStream("/rewrite/versions.properties")) {
+        if (versionProps == null) {
+            try (InputStream is = DefaultRewriteExtension.class.getResourceAsStream("/rewrite/versions.properties")) {
                 versionProps = new Properties();
                 versionProps.load(is);
-            } catch(IOException e) {
+            } catch (IOException e) {
                 throw new RuntimeException(e);
             }
         }
@@ -211,7 +211,7 @@ private Properties getVersionProps() {
      */
     @Override
     public String getRewriteVersion() {
-        if(rewriteVersion == null) {
+        if (rewriteVersion == null) {
             return getVersionProps().getProperty("org.openrewrite:rewrite-core");
         }
         return rewriteVersion;
@@ -219,7 +219,7 @@ public String getRewriteVersion() {
 
     @Override
     public String getRewritePolyglotVersion() {
-        if(rewriteVersion == null) {
+        if (rewriteVersion == null) {
             return getVersionProps().getProperty("org.openrewrite:rewrite-polyglot");
         }
         return rewriteVersion;
@@ -228,7 +228,7 @@ public String getRewritePolyglotVersion() {
     private String rewriteGradleModelVersion;
     @Override
     public String getRewriteGradleModelVersion() {
-        if(rewriteGradleModelVersion == null) {
+        if (rewriteGradleModelVersion == null) {
             rewriteGradleModelVersion = getVersionProps().getProperty("org.openrewrite.gradle.tooling:model");
         }
         return rewriteGradleModelVersion;
@@ -237,7 +237,7 @@ public String getRewriteGradleModelVersion() {
     private String rewriteKotlinVersion;
     @Override
     public String getRewriteKotlinVersion() {
-        if(rewriteKotlinVersion == null) {
+        if (rewriteKotlinVersion == null) {
             rewriteKotlinVersion = getVersionProps().getProperty("org.openrewrite:rewrite-kotlin");
         }
         return rewriteKotlinVersion;
@@ -384,7 +384,7 @@ public String getJacksonModuleKotlinVersion() {
 
     @Override
     public boolean getThrowOnParseFailures() {
-        if(project.getProperties().containsKey("rewrite.throwOnParseFailures")) {
+        if (project.getProperties().containsKey("rewrite.throwOnParseFailures")) {
             return true;
         }
         return throwOnParseFailures;
diff --git a/plugin/src/main/java/org/openrewrite/gradle/DelegatingProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/DelegatingProjectParser.java
index 77ae7fac4..2b33d8726 100755
--- a/plugin/src/main/java/org/openrewrite/gradle/DelegatingProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/DelegatingProjectParser.java
@@ -54,7 +54,7 @@ public DelegatingProjectParser(Project project, RewriteExtension extension, Set<
                     .getResource("/org/openrewrite/gradle/isolated/DefaultProjectParser.class")
                     .toString());
             classpathUrls.add(currentJar);
-            if(rewriteClassLoader == null || !classpathUrls.equals(rewriteClasspath)) {
+            if (rewriteClassLoader == null || !classpathUrls.equals(rewriteClasspath)) {
                 if (rewriteClassLoader != null) {
                     rewriteClassLoader.close();
                 }
diff --git a/plugin/src/main/java/org/openrewrite/gradle/SanitizedMarkerPrinter.java b/plugin/src/main/java/org/openrewrite/gradle/SanitizedMarkerPrinter.java
index 0d89b75af..131c01f41 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/SanitizedMarkerPrinter.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/SanitizedMarkerPrinter.java
@@ -29,7 +29,7 @@
 public class SanitizedMarkerPrinter implements PrintOutputCapture.MarkerPrinter {
     @Override
     public String beforeSyntax(Marker marker, Cursor cursor, UnaryOperator<String> commentWrapper) {
-        if(marker instanceof SearchResult) {
+        if (marker instanceof SearchResult) {
             return DEFAULT.beforeSyntax(marker, cursor, commentWrapper);
         }
         return "";
@@ -37,7 +37,7 @@ public String beforeSyntax(Marker marker, Cursor cursor, UnaryOperator<String> c
 
     @Override
     public String afterSyntax(Marker marker, Cursor cursor, UnaryOperator<String> commentWrapper) {
-        if(marker instanceof SearchResult) {
+        if (marker instanceof SearchResult) {
             return DEFAULT.afterSyntax(marker, cursor, commentWrapper);
         }
         return "";
diff --git a/plugin/src/main/java/org/openrewrite/gradle/TimeUtils.java b/plugin/src/main/java/org/openrewrite/gradle/TimeUtils.java
index 063101748..271c5194b 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/TimeUtils.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/TimeUtils.java
@@ -27,39 +27,39 @@ public static String prettyPrint(Duration duration) {
         StringBuilder result = new StringBuilder();
         long days = duration.getSeconds() / SECONDS_PER_DAY;
         boolean startedPrinting = false;
-        if(days > 0) {
+        if (days > 0) {
             startedPrinting = true;
             result.append(days);
             result.append(" day");
-            if(days != 1) {
+            if (days != 1) {
                 result.append("s");
             }
             result.append(" ");
         }
 
-        long hours =  duration.toHours() % 24;
-        if(startedPrinting || hours > 0) {
+        long hours = duration.toHours() % 24;
+        if (startedPrinting || hours > 0) {
             startedPrinting = true;
             result.append(hours);
             result.append(" hour");
-            if(hours != 1) {
+            if (hours != 1) {
                 result.append("s");
             }
             result.append(" ");
         }
 
         long minutes = (duration.getSeconds() / SECONDS_PER_MINUTE) % MINUTES_PER_HOUR;
-        if(startedPrinting || minutes > 0) {
+        if (startedPrinting || minutes > 0) {
             result.append(minutes);
             result.append(" minute");
-            if(minutes != 1) {
+            if (minutes != 1) {
                 result.append("s");
             }
             result.append(" ");
         }
 
         long seconds = duration.getSeconds() % SECONDS_PER_MINUTE;
-        if(startedPrinting || seconds > 0) {
+        if (startedPrinting || seconds > 0) {
             result.append(seconds);
             result.append(" second");
             if (seconds != 1) {
@@ -71,7 +71,7 @@ public static String prettyPrint(Duration duration) {
         long millis = duration.getNano() / 1000_000;
         result.append(millis);
         result.append(" millisecond");
-        if(millis != 1) {
+        if (millis != 1) {
             result.append("s");
         }
 
diff --git a/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt b/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
index a0acd9647..6b147d45e 100644
--- a/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
+++ b/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
@@ -77,51 +77,51 @@ class GradleProjectSpec(
     fun build(): GradleProjectSpec {
         dir.mkdirs()
 
-        if(settingsGradle != null) {
+        if (settingsGradle != null) {
             File(dir, "settings.gradle").writeText(settingsGradle!!)
         }
 
-        if(groovyBuildScript != null) {
+        if (groovyBuildScript != null) {
             File(dir, "build.gradle").writeText(groovyBuildScript!!)
         }
 
-        if(rewriteYaml != null) {
+        if (rewriteYaml != null) {
             File(dir, "rewrite.yml").writeText(rewriteYaml!!)
         }
 
-        if(checkstyleXml != null) {
-            File(dir, "config/checkstyle/checkstyle.xml").apply {
+        if (checkstyleXml != null) {
+            File(dir, "config/checkstyle/checkstyle.xml").apply{ 
                 parentFile.mkdirs()
                 writeText(checkstyleXml!!)
             }
         }
 
-        for(props in propertiesFiles.entries) {
-            File(dir, props.key).apply {
+        for (props in propertiesFiles.entries) {
+            File(dir, props.key).apply{ 
                 parentFile.mkdirs()
                 writeText(props.value)
             }
         }
 
-        for(text in textFiles.entries) {
-            File(dir, text.key).apply {
+        for (text in textFiles.entries) {
+            File(dir, text.key).apply{ 
                 parentFile.mkdirs()
                 writeText(text.value)
             }
         }
 
-        for(sourceSet in sourceSets) {
+        for (sourceSet in sourceSets) {
             sourceSet.build(File(dir, "src"))
         }
 
         val settings = File(dir, "settings.gradle")
         val settingsText = "rootProject.name = \"${dir.name}\"\n"
-        if(subprojects.isEmpty()) {
+        if (subprojects.isEmpty()) {
             settings.writeText("rootProject.name = \"${dir.name}\"\n")
         } else {
-            val subprojectsDeclarations = subprojects.joinToString("\n") { subproject -> "include('${subproject.dir.name}')" }
+            val subprojectsDeclarations = subprojects.joinToString("\n") { subproject  ->  "include('${subproject.dir.name}')" }
             settings.writeText(settingsText + subprojectsDeclarations)
-            for(subproject in subprojects) {
+            for (subproject in subprojects) {
                 subproject.build()
             }
         }
@@ -161,8 +161,8 @@ class GradleSourceSetSpec(
     @Suppress("RegExpSimplifiable")
     fun build(dir: File): GradleSourceSetSpec {
         dir.mkdirs()
-        for(javaSource in javaSources) {
-            val peckage = if(javaSource.startsWith("package")) {
+        for (javaSource in javaSources) {
+            val peckage = if (javaSource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+);".toRegex(RegexOption.MULTILINE)
                     .find(javaSource)!!
                     .groupValues[1]
@@ -170,18 +170,18 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(javaSource)!!.groupValues[2]
-            val path = if(peckage.isEmpty()) {
+            val path = if (peckage.isEmpty()) {
                 "$name/java/$clazz.java"
             } else {
                 "$name/java/$peckage/$clazz.java"
             }
-            File(dir, path).apply {
+            File(dir, path).apply{ 
                 parentFile.mkdirs()
                 writeText(javaSource)
             }
         }
-        for(kotlinSource in kotlinSources) {
-            val peckage = if(kotlinSource.startsWith("package")) {
+        for (kotlinSource in kotlinSources) {
+            val peckage = if (kotlinSource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+)".toRegex(RegexOption.MULTILINE)
                     .find(kotlinSource)!!
                     .groupValues[1]
@@ -189,18 +189,18 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(kotlinSource)!!.groupValues[2]
-            val path = if(peckage.isEmpty()) {
+            val path = if (peckage.isEmpty()) {
                 "$name/kotlin/$clazz.kt"
             } else {
                 "$name/kotlin/$peckage/$clazz.kt"
             }
-            File(dir, path).apply {
+            File(dir, path).apply{ 
                 parentFile.mkdirs()
                 writeText(kotlinSource)
             }
         }
-        for(groovySource in groovyClasses) {
-            val peckage = if(groovySource.startsWith("package")) {
+        for (groovySource in groovyClasses) {
+            val peckage = if (groovySource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+);?".toRegex(RegexOption.MULTILINE)
                     .find(groovySource)!!
                     .groupValues[1]
@@ -208,27 +208,27 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(groovySource)!!.groupValues[2]
-            val path = if(peckage.isEmpty()) {
+            val path = if (peckage.isEmpty()) {
                 "$name/groovy/$clazz.groovy"
             } else {
                 "$name/groovy/$peckage/$clazz.groovy"
             }
-            File(dir, path).apply {
+            File(dir, path).apply{ 
                 parentFile.mkdirs()
                 writeText(groovySource)
             }
         }
-        if(propertiesFiles.isNotEmpty()) {
-            for(props in propertiesFiles.entries) {
-                File(dir, "$name/resources/${props.key}").apply {
+        if (propertiesFiles.isNotEmpty()) {
+            for (props in propertiesFiles.entries) {
+                File(dir, "$name/resources/${props.key}").apply{ 
                     parentFile.mkdirs()
                     writeText(props.value)
                 }
             }
         }
-        if(yamlFiles.isNotEmpty()) {
-            for(yaml in yamlFiles.entries) {
-                File(dir, "$name/resources/${yaml.key}").apply {
+        if (yamlFiles.isNotEmpty()) {
+            for (yaml in yamlFiles.entries) {
+                File(dir, "$name/resources/${yaml.key}").apply{ 
                     parentFile.mkdirs()
                     writeText(yaml.value)
                 }
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDiscoverTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDiscoverTest.kt
index f2bd14a59..0e17b2d89 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDiscoverTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDiscoverTest.kt
@@ -28,7 +28,7 @@ class RewriteDiscoverTest : RewritePluginTest {
     fun `rewriteDiscover prints recipes from external dependencies`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle("""
                 plugins {
                     id("java")
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDryRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDryRunTest.kt
index 7a2d37da7..254e17772 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDryRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteDryRunTest.kt
@@ -35,7 +35,7 @@ class RewriteDryRunTest : RewritePluginTest {
                 }public static void main(String[] args) {   sayGoodbye(); }
             }
         """.trimIndent()
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.gradle.SayHello
@@ -65,7 +65,7 @@ class RewriteDryRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.gradle.SayHello", "org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java(helloWorld)
             }
         }
@@ -82,7 +82,7 @@ class RewriteDryRunTest : RewritePluginTest {
     fun `A recipe with optional configuration can be activated directly`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle("""
                 plugins {
                     id("java")
@@ -97,7 +97,7 @@ class RewriteDryRunTest : RewritePluginTest {
                     }
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package org.openrewrite.before;
                 
@@ -127,7 +127,7 @@ class RewriteDryRunTest : RewritePluginTest {
     @DisabledIf("lessThanGradle6_1")
     @Test
     fun testMultiplatform(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle("""
                 plugins {
                     id("java")
@@ -177,7 +177,7 @@ class RewriteDryRunTest : RewritePluginTest {
                 }
                 rootProject.name = "example"
             """)
-            sourceSet("commonMain") {
+            sourceSet("commonMain") { 
                 kotlin("""
                     class HelloWorld {
                         fun sayHello() {
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
index 7ff56fb66..d2b7f9e9b 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
@@ -29,7 +29,7 @@ interface RewritePluginTest {
         GradleRunner.create()
             .withDebug(ManagementFactory.getRuntimeMXBean().inputArguments.toString().indexOf("-agentlib:jdwp") > 0)
             .withProjectDir(testDir)
-            .apply {
+            .apply{ 
                 if (gradleVersion != null) {
                     withGradleVersion(gradleVersion)
                 }
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index fd3052a85..d77f32793 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -40,7 +40,7 @@ class RewriteRunTest : RewritePluginTest {
         // Gradle provides no control over how it arbitrarily orders its classpath
         // So even if isolation isn't working at all, this could pass if it happens to put the rewrite's required version
         // of jackson first on the classpath.
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle("""
                 buildscript {
                     repositories {
@@ -69,7 +69,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("test") {
+            sourceSet("test") { 
                 java("""
                     package com.foo;
                     
@@ -89,7 +89,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `rewriteRun will alter the source file according to the provided active recipe`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.gradle.SayHello
@@ -119,7 +119,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.gradle.SayHello", "org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package org.openrewrite.before;
                     
@@ -170,7 +170,7 @@ class RewriteRunTest : RewritePluginTest {
                     public void passes() { }
                 }
         """.trimIndent()
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.FormatAndAddProperty
@@ -212,8 +212,8 @@ class RewriteRunTest : RewritePluginTest {
                     }
                 }
             """)
-            subproject("a") {
-                sourceSet("test") {
+            subproject("a") { 
+                sourceSet("test") { 
                     java("""
                         package com.foo;
             
@@ -228,8 +228,8 @@ class RewriteRunTest : RewritePluginTest {
                     propertiesFile("test.properties", "foo=baz\n")
                 }
             }
-            subproject("b") {
-                sourceSet("test") {
+            subproject("b") { 
+                sourceSet("test") { 
                     java(bTestClassExpected)
                 }
             }
@@ -265,7 +265,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Checkstyle configuration is applied as a style`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             checkstyleXml("""
                 <!DOCTYPE module PUBLIC
                     "-//Checkstyle//DTD Checkstyle Configuration 1.2//EN"
@@ -299,7 +299,7 @@ class RewriteRunTest : RewritePluginTest {
                     rewrite("org.openrewrite.recipe:rewrite-static-analysis:1.0.4")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package com.foo;
                     
@@ -314,7 +314,7 @@ class RewriteRunTest : RewritePluginTest {
             }
         }
 
-        val result = runGradle(projectDir,"rewriteRun")
+        val result = runGradle(projectDir, "rewriteRun")
         val rewriteRunResult = result.task(":rewriteRun")!!
 
         assertThat(rewriteRunResult.outcome).isEqualTo(TaskOutcome.SUCCESS)
@@ -338,7 +338,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `can apply non-java recipe to files inside and outside of java resources directories`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: com.example.RenameSam
@@ -368,7 +368,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
             """)
             propertiesFile("outside-of-sourceset.properties", "sam=true\n")
-            sourceSet("main") {
+            sourceSet("main") { 
                 propertiesFile("in-sourceset.properties", "sam=true\n")
             }
         }
@@ -385,7 +385,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Recipes that generate sources have those sources written out to disk successfully`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.AddGradleWrapper
@@ -442,7 +442,7 @@ class RewriteRunTest : RewritePluginTest {
     fun gradleDependencyManagement(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.RemoveJacksonCore
@@ -518,7 +518,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun mergeConfiguredAndAutodetectedStyles(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             propertiesFile("gradle.properties", "systemProp.rewrite.activeStyles=org.openrewrite.testStyle")
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/style
@@ -545,7 +545,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 // Uses spaces, to be converted to tabs
                 java("""
                     package com.foo;
@@ -588,7 +588,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun reformatToIntelliJStyle(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle("""
                 plugins {
                     id("java")
@@ -608,7 +608,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeStyle("org.openrewrite.java.IntelliJ")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package com.foo;
                     
@@ -663,7 +663,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun groovySourceGetsTypesFromJavaSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.FindA
@@ -696,7 +696,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package com.foo;
                     
@@ -738,7 +738,7 @@ class RewriteRunTest : RewritePluginTest {
     @DisabledIf("lessThanGradle6_1")
     @Test
     fun kotlinSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             buildGradle(
                 """
                 plugins {
@@ -765,7 +765,7 @@ class RewriteRunTest : RewritePluginTest {
                   - org.openrewrite.java.search.FindTypes:
                       fullyQualifiedTypeName: kotlin.String
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 kotlin("""
                     package com.foo
                     
@@ -789,7 +789,7 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/128")
     @Test
     fun deleteEmptyDirectory(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
               name: org.openrewrite.test.DeleteFoo
@@ -836,26 +836,26 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun `build root and repository root do not need to be the same`(@TempDir repositoryRoot: File) {
-        repositoryRoot.apply {
-            resolve(".git").apply {
+        repositoryRoot.apply{ 
+            resolve(".git").apply{ 
                 mkdirs()
-                resolve("HEAD").apply {
+                resolve("HEAD").apply{ 
                     createNewFile()
                     writeText("ref: refs/heads/main")
                 }
-                resolve("objects").apply {
+                resolve("objects").apply{ 
                     mkdir()
                 }
-                resolve("refs").apply {
+                resolve("refs").apply{ 
                     mkdir()
                 }
-                resolve("reftable").apply {
+                resolve("reftable").apply{ 
                     mkdir()
                 }
             }
         }
-        val buildRoot = repositoryRoot.resolve("test-project").apply { mkdirs() }
-        gradleProject(buildRoot) {
+        val buildRoot = repositoryRoot.resolve("test-project").apply{  mkdirs() }
+        gradleProject(buildRoot) { 
             buildGradle("""
                 plugins {
                     id("java")
@@ -874,7 +874,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") {
+            sourceSet("main") { 
                 java("""
                     package org.openrewrite.before;
                 
@@ -918,20 +918,20 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/176")
     @Test
     fun runRecipeFromProjectDependency(@TempDir projectDir: File) {
-        gradleProject(projectDir) {
+        gradleProject(projectDir) { 
             settingsGradle("""
                 rootProject.name = 'multi-project-recipe'
 
                 include("recipe")
                 include("product")
             """)
-            subproject("recipe") {
+            subproject("recipe") { 
                 buildGradle("""
                     plugins { 
                         id("java")
                     }
                 """)
-                sourceSet("main") {
+                sourceSet("main") { 
                     yamlFile("META-INF/rewrite/recipe.yml", """
                         type: specs.openrewrite.org/v1beta/recipe
                         name: com.example.TextToSam
@@ -947,7 +947,7 @@ class RewriteRunTest : RewritePluginTest {
                     """)
                 }
             }
-            subproject("product") {
+            subproject("product") { 
                 buildGradle("""
                     plugins {
                         id("org.openrewrite.rewrite")
@@ -988,7 +988,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun overlappingSourceSet(@TempDir buildRoot: File) {
-        gradleProject(buildRoot) {
+        gradleProject(buildRoot) { 
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
               name: org.openrewrite.test.FindSneaky
@@ -1026,7 +1026,7 @@ class RewriteRunTest : RewritePluginTest {
                     testImplementation("org.projectlombok:lombok:latest.release")
                 }
             """)
-            sourceSet("test") {
+            sourceSet("test") { 
                 java("""
                     package com.foo;
                     
diff --git a/scripts/spring-petclinic-test.init.gradle b/scripts/spring-petclinic-test.init.gradle
index 6e3e02dd1..93d09cc05 100755
--- a/scripts/spring-petclinic-test.init.gradle
+++ b/scripts/spring-petclinic-test.init.gradle
@@ -1,62 +1,62 @@
-initscript {
-    repositories {
-        repositories {
+initscript{
+    repositories{
+        repositories{
             mavenLocal()
-            maven {
+            maven{
                 url = uri("https://oss.sonatype.org/content/repositories/snapshots")
             }
             mavenCentral()
         }
     }
-    dependencies {
+    dependencies{
         classpath("org.openrewrite:plugin:latest.integration")
     }
 }
 
-projectsEvaluated {
-    rootProject {
-        apply plugin: org.openrewrite.gradle.RewritePlugin
+projectsEvaluated{
+    rootProject{
+        applyplugin: org.openrewrite.gradle.RewritePlugin
 
-        repositories {
+        repositories{
             mavenLocal()
-            maven {
+            maven{
                 url = uri("https://oss.sonatype.org/content/repositories/snapshots")
             }
             mavenCentral()
         }
 
-        rewrite {
+        rewrite{
             failOnInvalidActiveRecipes = true
             activeRecipe("org.openrewrite.java.spring.boot2.SpringBoot1To2Migration")
         }
 
-        dependencies {
+        dependencies{
             rewrite("org.openrewrite.recipe:rewrite-spring:latest.integration")
         }
 
         tasks.create("validateRewrite") {
              dependsOn(tasks.getByName("rewriteDryRun"))
-             doLast {
+             doLast{
                  File patchFile = file("build/reports/rewrite/rewrite.patch")
-                 if(!patchFile.exists()) {
+                 if (!patchFile.exists()) {
                      throw new RuntimeException("Running rewrite dryRun failed to produce a patch report at " + patchFile.absolutePath);
                  }
 
                  // Spot-check for some expected changes
                  String patch = patchFile.text
-                 if(!patch.contains('+++ b/src/main/java/org/springframework/samples/petclinic/owner/OwnerController.java')) {
+                 if (!patch.contains('+++ b/src/main/java/org/springframework/samples/petclinic/owner/OwnerController.java')) {
                     throw new RuntimeException("Expected the recipe to make changes to OwnerController.java");
                  }
-                 if(!patch.contains('-    @RequestMapping(value = "/owners/what")\n+    @GetMapping("/owners/what")')) {
+                 if (!patch.contains('-    @RequestMapping(value = "/owners/what")\n+    @GetMapping("/owners/what")')) {
                      throw new RuntimeException("Expected the recipe to change @RequestMapping into @GetMapping")
                  }
-                 if(!patch.contains('-    public JCacheManagerCustomizer cacheManagerCustomizer() {\n+    JCacheManagerCustomizer cacheManagerCustomizer() {')) {
+                 if (!patch.contains('-    public JCacheManagerCustomizer cacheManagerCustomizer() {\n+    JCacheManagerCustomizer cacheManagerCustomizer() {')) {
                      throw new RuntimeException("Expected the recipe to reduce visibility of bean methods that don't need to be public")
                  }
-                 if(!patch.contains('-@RunWith(MockitoJUnitRunner.class)\n+@ExtendWith(MockitoExtension.class)\n public class PetTypeFormatterTests {')) {
+                 if (!patch.contains('-@RunWith(MockitoJUnitRunner.class)\n+@ExtendWith(MockitoExtension.class)\n public class PetTypeFormatterTests {')) {
                      throw new RuntimeException("Expected the recipe to swap MockitoJUnitRunner for MockitoExtension")
                  }
-                 if(!patch.contains('-spring.datasource.schema=classpath*:db/${database}/schema.sql\n' +
+                 if (!patch.contains('-spring.datasource.schema=classpath*:db/${database}/schema.sql\n' +
                          '-spring.datasource.data=classpath*:db/${database}/data.sql\n' +
                          '+spring.sql.init.schema-locations=classpath*:db/${database}/schema.sql\n' +
                          '+spring.sql.init.data-locations=classpath*:db/${database}/data.sql')) {

From 8c1986ca5420ad81a5eb7785240605db08d35cdc Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Thu, 28 Sep 2023 19:26:56 -0700
Subject: [PATCH 10/20] Handle partially-overlapping source sets better. Parse
 each directory exactly once.

---
 .../org/openrewrite/gradle/RewritePlugin.java |  2 +-
 .../gradle/isolated/DefaultProjectParser.java | 50 ++++++-----
 .../org/openrewrite/gradle/RewriteRunTest.kt  | 88 ++++++++++---------
 3 files changed, 73 insertions(+), 67 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
index 1549446dd..16c9534eb 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/RewritePlugin.java
@@ -118,7 +118,7 @@ private static void configureProject(Project project, RewriteExtension extension
                             return 2;
                         }
                     })).forEach(sourceSet -> {
-                        for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                        for (File file : sourceSet.getAllJava().getSourceDirectories().getFiles()) {
                             if (!sourceDirs.add(file.getAbsolutePath())) {
                                 Task compileTask = project.getTasks().getByPath(sourceSet.getCompileJavaTaskName());
                                 compileTask.setEnabled(false);
diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index bc8d72ce9..5f2819049 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -85,6 +85,7 @@
 import java.util.function.Consumer;
 import java.util.function.Supplier;
 import java.util.function.UnaryOperator;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import static java.util.Collections.*;
@@ -653,15 +654,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
             }
 
             Set<String> sourceDirs = new HashSet<>();
-            sourceSetLoop:
             for (SourceSet sourceSet : sourceSets) {
-                        // Detect SourceSets which overlap other sourceSets and disable the compilation task of the overlapping
-            // source set. Skip parsing directories already covered by another source set.
-                for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
-                    if (!sourceDirs.add(file.getAbsolutePath())) {
-                        continue sourceSetLoop;
-                    }
-                }
                 Stream<SourceFile> sourceSetSourceFiles = Stream.of();
                 int sourceSetSize = 0;
 
@@ -672,11 +665,24 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                         javaCompileTask.getSourceCompatibility(),
                         javaCompileTask.getTargetCompatibility());
 
-                List<Path> javaPaths = sourceSet.getAllJava().getFiles().stream()
-                        .filter(it -> it.isFile() && it.getName().endsWith(".java"))
-                        .map(File::toPath)
+                List<Path> unparsedSources = sourceSet.getAllSource()
+                        .getSourceDirectories()
+                        .filter(it -> it.exists() && !alreadyParsed.contains(baseDir.relativize(it.toPath())))
+                        .getFiles()
+                        .stream()
+                        .flatMap(sourceDir -> {
+                            try {
+                                return Files.walk(sourceDir.toPath());
+                            } catch (IOException e) {
+                                throw new UncheckedIOException(e);
+                            }
+                        })
+                        .filter(Files::isRegularFile)
                         .map(Path::toAbsolutePath)
                         .map(Path::normalize)
+                        .collect(Collectors.toList());
+                List<Path> javaPaths = unparsedSources.stream()
+                        .filter(it -> it.toString().endsWith(".java"))
                         .collect(toList());
 
                 // classpath doesn't include the transitive dependencies of the implementation configuration
@@ -731,11 +737,8 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 if (subproject.getPlugins().hasPlugin("org.jetbrains.kotlin.jvm")) {
-                    List<Path> kotlinPaths = sourceSet.getAllSource().getFiles().stream()
-                            .filter(it -> it.isFile() && it.getName().endsWith(".kt"))
-                            .map(File::toPath)
-                            .map(Path::toAbsolutePath)
-                            .map(Path::normalize)
+                    List<Path> kotlinPaths = unparsedSources.stream()
+                            .filter(it -> it.toString().endsWith(".kt"))
                             .collect(toList());
 
                     if (!kotlinPaths.isEmpty()) {
@@ -762,13 +765,9 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                         logger.info("Scanned {} Kotlin sources in {}/{}", kotlinPaths.size(), subproject.getPath(), sourceSet.getName());
                     }
                 }
-
                 if (subproject.getPlugins().hasPlugin(GroovyPlugin.class)) {
-                    List<Path> groovyPaths = sourceSet.getAllSource().getFiles().stream()
-                            .filter(it -> it.isFile() && it.getName().endsWith(".groovy"))
-                            .map(File::toPath)
-                            .map(Path::toAbsolutePath)
-                            .map(Path::normalize)
+                    List<Path> groovyPaths = unparsedSources.stream()
+                            .filter(it -> it.toString().endsWith(".groovy"))
                             .collect(toList());
 
                     if (!groovyPaths.isEmpty()) {
@@ -805,7 +804,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
-                    if (resourcesDir.exists()) {
+                    if (resourcesDir.exists() && !alreadyParsed.contains(baseDir.relativize(resourcesDir.toPath()))) {
                         OmniParser omniParser = omniParser(alreadyParsed);
                         List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
@@ -819,6 +818,11 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 JavaSourceSet sourceSetProvenance = JavaSourceSet.build(sourceSet.getName(), dependencyPaths, javaTypeCache, false);
                 sourceFileStream = sourceFileStream.concat(sourceSetSourceFiles.map(addProvenance(sourceSetProvenance)), sourceSetSize);
+                // Some source sets get misconfigured to have the same directories as other source sets
+                // This causes duplicate source files to be parsed, so once a source set has been parsed exclude it from future parsing
+                for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
+                    alreadyParsed.add(baseDir.relativize(file.toPath()));
+                }
             }
             SourceFileStream gradleFiles = parseGradleFiles(exclusions, alreadyParsed, ctx);
             sourceFileStream = sourceFileStream.concat(gradleFiles, gradleFiles.size());
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index d77f32793..8aee56aaa 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -40,7 +40,7 @@ class RewriteRunTest : RewritePluginTest {
         // Gradle provides no control over how it arbitrarily orders its classpath
         // So even if isolation isn't working at all, this could pass if it happens to put the rewrite's required version
         // of jackson first on the classpath.
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle("""
                 buildscript {
                     repositories {
@@ -69,7 +69,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("test") { 
+            sourceSet("test") {
                 java("""
                     package com.foo;
                     
@@ -89,7 +89,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `rewriteRun will alter the source file according to the provided active recipe`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.gradle.SayHello
@@ -119,7 +119,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.gradle.SayHello", "org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package org.openrewrite.before;
                     
@@ -170,7 +170,7 @@ class RewriteRunTest : RewritePluginTest {
                     public void passes() { }
                 }
         """.trimIndent()
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.FormatAndAddProperty
@@ -212,8 +212,8 @@ class RewriteRunTest : RewritePluginTest {
                     }
                 }
             """)
-            subproject("a") { 
-                sourceSet("test") { 
+            subproject("a") {
+                sourceSet("test") {
                     java("""
                         package com.foo;
             
@@ -228,8 +228,8 @@ class RewriteRunTest : RewritePluginTest {
                     propertiesFile("test.properties", "foo=baz\n")
                 }
             }
-            subproject("b") { 
-                sourceSet("test") { 
+            subproject("b") {
+                sourceSet("test") {
                     java(bTestClassExpected)
                 }
             }
@@ -265,7 +265,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Checkstyle configuration is applied as a style`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             checkstyleXml("""
                 <!DOCTYPE module PUBLIC
                     "-//Checkstyle//DTD Checkstyle Configuration 1.2//EN"
@@ -299,7 +299,7 @@ class RewriteRunTest : RewritePluginTest {
                     rewrite("org.openrewrite.recipe:rewrite-static-analysis:1.0.4")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -338,7 +338,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `can apply non-java recipe to files inside and outside of java resources directories`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: com.example.RenameSam
@@ -368,7 +368,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
             """)
             propertiesFile("outside-of-sourceset.properties", "sam=true\n")
-            sourceSet("main") { 
+            sourceSet("main") {
                 propertiesFile("in-sourceset.properties", "sam=true\n")
             }
         }
@@ -385,7 +385,7 @@ class RewriteRunTest : RewritePluginTest {
     fun `Recipes that generate sources have those sources written out to disk successfully`(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.AddGradleWrapper
@@ -442,7 +442,7 @@ class RewriteRunTest : RewritePluginTest {
     fun gradleDependencyManagement(
         @TempDir projectDir: File
     ) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.RemoveJacksonCore
@@ -518,7 +518,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun mergeConfiguredAndAutodetectedStyles(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             propertiesFile("gradle.properties", "systemProp.rewrite.activeStyles=org.openrewrite.testStyle")
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/style
@@ -545,7 +545,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 // Uses spaces, to be converted to tabs
                 java("""
                     package com.foo;
@@ -588,7 +588,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun reformatToIntelliJStyle(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle("""
                 plugins {
                     id("java")
@@ -608,7 +608,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeStyle("org.openrewrite.java.IntelliJ")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -663,7 +663,7 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun groovySourceGetsTypesFromJavaSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.FindA
@@ -696,7 +696,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package com.foo;
                     
@@ -738,7 +738,7 @@ class RewriteRunTest : RewritePluginTest {
     @DisabledIf("lessThanGradle6_1")
     @Test
     fun kotlinSource(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             buildGradle(
                 """
                 plugins {
@@ -765,7 +765,7 @@ class RewriteRunTest : RewritePluginTest {
                   - org.openrewrite.java.search.FindTypes:
                       fullyQualifiedTypeName: kotlin.String
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 kotlin("""
                     package com.foo
                     
@@ -789,7 +789,7 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/128")
     @Test
     fun deleteEmptyDirectory(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
               name: org.openrewrite.test.DeleteFoo
@@ -836,26 +836,26 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun `build root and repository root do not need to be the same`(@TempDir repositoryRoot: File) {
-        repositoryRoot.apply{ 
-            resolve(".git").apply{ 
+        repositoryRoot.apply{
+            resolve(".git").apply{
                 mkdirs()
-                resolve("HEAD").apply{ 
+                resolve("HEAD").apply{
                     createNewFile()
                     writeText("ref: refs/heads/main")
                 }
-                resolve("objects").apply{ 
+                resolve("objects").apply{
                     mkdir()
                 }
-                resolve("refs").apply{ 
+                resolve("refs").apply{
                     mkdir()
                 }
-                resolve("reftable").apply{ 
+                resolve("reftable").apply{
                     mkdir()
                 }
             }
         }
         val buildRoot = repositoryRoot.resolve("test-project").apply{  mkdirs() }
-        gradleProject(buildRoot) { 
+        gradleProject(buildRoot) {
             buildGradle("""
                 plugins {
                     id("java")
@@ -874,7 +874,7 @@ class RewriteRunTest : RewritePluginTest {
                     activeRecipe("org.openrewrite.java.format.AutoFormat")
                 }
             """)
-            sourceSet("main") { 
+            sourceSet("main") {
                 java("""
                     package org.openrewrite.before;
                 
@@ -918,20 +918,20 @@ class RewriteRunTest : RewritePluginTest {
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/176")
     @Test
     fun runRecipeFromProjectDependency(@TempDir projectDir: File) {
-        gradleProject(projectDir) { 
+        gradleProject(projectDir) {
             settingsGradle("""
                 rootProject.name = 'multi-project-recipe'
 
                 include("recipe")
                 include("product")
             """)
-            subproject("recipe") { 
+            subproject("recipe") {
                 buildGradle("""
                     plugins { 
                         id("java")
                     }
                 """)
-                sourceSet("main") { 
+                sourceSet("main") {
                     yamlFile("META-INF/rewrite/recipe.yml", """
                         type: specs.openrewrite.org/v1beta/recipe
                         name: com.example.TextToSam
@@ -947,7 +947,7 @@ class RewriteRunTest : RewritePluginTest {
                     """)
                 }
             }
-            subproject("product") { 
+            subproject("product") {
                 buildGradle("""
                     plugins {
                         id("org.openrewrite.rewrite")
@@ -988,15 +988,16 @@ class RewriteRunTest : RewritePluginTest {
 
     @Test
     fun overlappingSourceSet(@TempDir buildRoot: File) {
-        gradleProject(buildRoot) { 
+        gradleProject(buildRoot) {
             rewriteYaml("""
               type: specs.openrewrite.org/v1beta/recipe
-              name: org.openrewrite.test.FindSneaky
-              displayName: Find lombok SneakyThrows annotation
-              description: Find lombok SneakyThrows annotation
+              name: org.openrewrite.Overlaps
+              displayName: Find overlaps
+              description: Find lombok SneakyThrows annotation and duplicate source files
               recipeList:
                 - org.openrewrite.java.search.FindTypes:
                     fullyQualifiedTypeName: lombok.SneakyThrows
+                - org.openrewrite.FindDuplicateSourceFiles
             """)
             buildGradle("""
                 plugins { 
@@ -1017,16 +1018,17 @@ class RewriteRunTest : RewritePluginTest {
                         java.srcDir("src/test/java")
                     }
                 }
-                
+
                 rewrite {
-                    activeRecipe("org.openrewrite.test.FindSneaky")
+                    activeRecipe("org.openrewrite.Overlaps")
                 }
                 
                 dependencies {
+                    rewrite("org.openrewrite.recipe:rewrite-all:latest.integration")
                     testImplementation("org.projectlombok:lombok:latest.release")
                 }
             """)
-            sourceSet("test") { 
+            sourceSet("test") {
                 java("""
                     package com.foo;
                     

From 2eaa819a99cb55df469c05b4d6f7b3dc79494b04 Mon Sep 17 00:00:00 2001
From: Joan Viladrosa <joan@moderne.io>
Date: Fri, 29 Sep 2023 10:09:46 +0200
Subject: [PATCH 11/20] added log message for active styles (#232)

---
 .../org/openrewrite/gradle/isolated/DefaultProjectParser.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 5f2819049..78a34c559 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -622,6 +622,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
             logger.lifecycle("Scanning sources in project {}", subproject.getPath());
             List<NamedStyles> styles = getStyles();
+            logger.lifecycle("Using active styles {}", styles.stream().map(NamedStyles::getName).collect(toList()));
             @SuppressWarnings("deprecation")
             JavaPluginConvention javaConvention = subproject.getConvention().findPlugin(JavaPluginConvention.class);
             List<SourceSet> sourceSets;

From 6c9033e14058ebccd0613cbdd8299cbc76a7eec1 Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 29 Sep 2023 12:26:20 -0700
Subject: [PATCH 12/20] Further efforts to parse every source exactly once

---
 .../gradle/isolated/DefaultProjectParser.java    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 78a34c559..5c493c5f3 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -275,7 +275,6 @@ public Collection<Path> listSources() {
         if (javaConvention != null) {
             for (SourceSet sourceSet : javaConvention.getSourceSets()) {
                 sourceSet.getAllSource().getFiles().stream()
-                        .filter(it -> it.isFile() && (it.getName().endsWith(".java") || it.getName().endsWith(".kt")))
                         .map(File::toPath)
                         .map(Path::toAbsolutePath)
                         .map(Path::normalize)
@@ -668,7 +667,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 List<Path> unparsedSources = sourceSet.getAllSource()
                         .getSourceDirectories()
-                        .filter(it -> it.exists() && !alreadyParsed.contains(baseDir.relativize(it.toPath())))
+                        .filter(it -> it.exists() && !alreadyParsed.contains(it.toPath()))
                         .getFiles()
                         .stream()
                         .flatMap(sourceDir -> {
@@ -681,9 +680,10 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                         .filter(Files::isRegularFile)
                         .map(Path::toAbsolutePath)
                         .map(Path::normalize)
+                        .distinct()
                         .collect(Collectors.toList());
                 List<Path> javaPaths = unparsedSources.stream()
-                        .filter(it -> it.toString().endsWith(".java"))
+                        .filter(it -> it.toString().endsWith(".java") && !alreadyParsed.contains(it))
                         .collect(toList());
 
                 // classpath doesn't include the transitive dependencies of the implementation configuration
@@ -805,7 +805,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
-                    if (resourcesDir.exists() && !alreadyParsed.contains(baseDir.relativize(resourcesDir.toPath()))) {
+                    if (resourcesDir.exists() && !alreadyParsed.contains(resourcesDir.toPath())) {
                         OmniParser omniParser = omniParser(alreadyParsed);
                         List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
@@ -822,7 +822,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 // Some source sets get misconfigured to have the same directories as other source sets
                 // This causes duplicate source files to be parsed, so once a source set has been parsed exclude it from future parsing
                 for (File file : sourceSet.getAllSource().getSourceDirectories().getFiles()) {
-                    alreadyParsed.add(baseDir.relativize(file.toPath()));
+                    alreadyParsed.add(file.toPath());
                 }
             }
             SourceFileStream gradleFiles = parseGradleFiles(exclusions, alreadyParsed, ctx);
@@ -892,7 +892,7 @@ private SourceFileStream parseGradleFiles(
                     gradleFileCount++;
                 }
                 sourceFiles = sourceFiles.map(sourceFile -> sourceFile.withMarkers(sourceFile.getMarkers().add(gp)));
-                alreadyParsed.add(buildScriptPath);
+                alreadyParsed.add(project.getBuildscript().getSourceFile().toPath());
             }
         }
 
@@ -920,7 +920,7 @@ private SourceFileStream parseGradleFiles(
                                     return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
                                 }));
                 gradleFileCount++;
-                alreadyParsed.add(settingsPath);
+                alreadyParsed.add(settingsGradleFile.toPath());
             } else if (settingsGradleKtsFile.exists()) {
                 Path settingsPath = baseDir.relativize(settingsGradleKtsFile.toPath());
                 sourceFiles = Stream.concat(
@@ -934,7 +934,7 @@ private SourceFileStream parseGradleFiles(
                                     return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
                                 }));
                 gradleFileCount++;
-                alreadyParsed.add(settingsPath);
+                alreadyParsed.add(settingsGradleKtsFile.toPath());
             }
         }
 

From c8ef7d0ab9f5bb4563ffb1150d14332c843ebe4a Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 29 Sep 2023 16:54:32 -0700
Subject: [PATCH 13/20] Temporarily pin versions because latest.release isn't
 getting the latest, for reasons which are unclear to me

---
 plugin/build.gradle.kts | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/plugin/build.gradle.kts b/plugin/build.gradle.kts
index 003ddf497..4ad284e60 100644
--- a/plugin/build.gradle.kts
+++ b/plugin/build.gradle.kts
@@ -7,7 +7,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import java.util.*
 
 plugins {
-    kotlin("jvm") version("1.8.0")
+    kotlin("jvm") version("1.9.0")
     id("com.gradle.plugin-publish") version "1.1.0"
     id("com.github.hierynomus.license") version "0.16.1"
 }
@@ -89,7 +89,7 @@ tasks.withType<KotlinCompile>().configureEach {
 val rewriteDependencies = configurations.create("rewriteDependencies")
 
 dependencies {
-    "rewriteDependencies"(platform("org.openrewrite:rewrite-bom:$latest"))
+    "rewriteDependencies"(platform("org.openrewrite:rewrite-bom:8.6.2"))
     "rewriteDependencies"("org.openrewrite:rewrite-core")
     "rewriteDependencies"("org.openrewrite:rewrite-hcl")
     "rewriteDependencies"("org.openrewrite:rewrite-java")
@@ -97,35 +97,35 @@ dependencies {
     "rewriteDependencies"("org.openrewrite:rewrite-java-11")
     "rewriteDependencies"("org.openrewrite:rewrite-java-8")
     "rewriteDependencies"("org.openrewrite:rewrite-json")
-    "rewriteDependencies"("org.openrewrite:rewrite-kotlin:$latest")
+    "rewriteDependencies"("org.openrewrite:rewrite-kotlin:1.4.11")
     "rewriteDependencies"("org.openrewrite:rewrite-xml")
     "rewriteDependencies"("org.openrewrite:rewrite-yaml")
     "rewriteDependencies"("org.openrewrite:rewrite-properties")
     "rewriteDependencies"("org.openrewrite:rewrite-protobuf")
     "rewriteDependencies"("org.openrewrite:rewrite-groovy")
     "rewriteDependencies"("org.openrewrite:rewrite-gradle")
-    "rewriteDependencies"("org.openrewrite:rewrite-polyglot:$latest")
-    "rewriteDependencies"("org.openrewrite.gradle.tooling:model:$latest")
+    "rewriteDependencies"("org.openrewrite:rewrite-polyglot:1.6.1")
+    "rewriteDependencies"("org.openrewrite.gradle.tooling:model:1.3.1")
     "rewriteDependencies"("org.openrewrite:rewrite-maven")
     // Newer versions of checkstyle are compiled with a newer version of Java than is supported with gradle 4.x
     @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     "rewriteDependencies"("com.puppycrawl.tools:checkstyle:9.3")
     "rewriteDependencies"("com.fasterxml.jackson.module:jackson-module-kotlin:latest.release")
 
-    implementation(platform("org.openrewrite:rewrite-bom:$latest"))
+    implementation(platform("org.openrewrite:rewrite-bom:8.6.2"))
     compileOnly("org.openrewrite:rewrite-core")
     compileOnly("org.openrewrite:rewrite-gradle")
-    compileOnly("org.openrewrite.gradle.tooling:model:$latest")
+    compileOnly("org.openrewrite.gradle.tooling:model:1.3.1")
     compileOnly("org.openrewrite:rewrite-groovy")
     compileOnly("org.openrewrite:rewrite-hcl")
     compileOnly("org.openrewrite:rewrite-java")
     compileOnly("org.openrewrite:rewrite-json")
-    compileOnly("org.openrewrite:rewrite-kotlin:$latest")
+    compileOnly("org.openrewrite:rewrite-kotlin:1.4.11")
     compileOnly("org.openrewrite:rewrite-properties")
     compileOnly("org.openrewrite:rewrite-protobuf")
     compileOnly("org.openrewrite:rewrite-xml")
     compileOnly("org.openrewrite:rewrite-yaml")
-    compileOnly("org.openrewrite:rewrite-polyglot:$latest")
+    compileOnly("org.openrewrite:rewrite-polyglot:1.6.1")
     @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     compileOnly("com.puppycrawl.tools:checkstyle:9.3")
     compileOnly("org.jetbrains.kotlin:kotlin-gradle-plugin:latest.release")

From 0a0419b422041487610c598b9cf145e85639c53f Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 29 Sep 2023 17:00:10 -0700
Subject: [PATCH 14/20] Revert "Temporarily pin versions because latest.release
 isn't getting the latest, for reasons which are unclear to me"

This reverts commit c8ef7d0ab9f5bb4563ffb1150d14332c843ebe4a.
---
 plugin/build.gradle.kts | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/plugin/build.gradle.kts b/plugin/build.gradle.kts
index 4ad284e60..003ddf497 100644
--- a/plugin/build.gradle.kts
+++ b/plugin/build.gradle.kts
@@ -7,7 +7,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import java.util.*
 
 plugins {
-    kotlin("jvm") version("1.9.0")
+    kotlin("jvm") version("1.8.0")
     id("com.gradle.plugin-publish") version "1.1.0"
     id("com.github.hierynomus.license") version "0.16.1"
 }
@@ -89,7 +89,7 @@ tasks.withType<KotlinCompile>().configureEach {
 val rewriteDependencies = configurations.create("rewriteDependencies")
 
 dependencies {
-    "rewriteDependencies"(platform("org.openrewrite:rewrite-bom:8.6.2"))
+    "rewriteDependencies"(platform("org.openrewrite:rewrite-bom:$latest"))
     "rewriteDependencies"("org.openrewrite:rewrite-core")
     "rewriteDependencies"("org.openrewrite:rewrite-hcl")
     "rewriteDependencies"("org.openrewrite:rewrite-java")
@@ -97,35 +97,35 @@ dependencies {
     "rewriteDependencies"("org.openrewrite:rewrite-java-11")
     "rewriteDependencies"("org.openrewrite:rewrite-java-8")
     "rewriteDependencies"("org.openrewrite:rewrite-json")
-    "rewriteDependencies"("org.openrewrite:rewrite-kotlin:1.4.11")
+    "rewriteDependencies"("org.openrewrite:rewrite-kotlin:$latest")
     "rewriteDependencies"("org.openrewrite:rewrite-xml")
     "rewriteDependencies"("org.openrewrite:rewrite-yaml")
     "rewriteDependencies"("org.openrewrite:rewrite-properties")
     "rewriteDependencies"("org.openrewrite:rewrite-protobuf")
     "rewriteDependencies"("org.openrewrite:rewrite-groovy")
     "rewriteDependencies"("org.openrewrite:rewrite-gradle")
-    "rewriteDependencies"("org.openrewrite:rewrite-polyglot:1.6.1")
-    "rewriteDependencies"("org.openrewrite.gradle.tooling:model:1.3.1")
+    "rewriteDependencies"("org.openrewrite:rewrite-polyglot:$latest")
+    "rewriteDependencies"("org.openrewrite.gradle.tooling:model:$latest")
     "rewriteDependencies"("org.openrewrite:rewrite-maven")
     // Newer versions of checkstyle are compiled with a newer version of Java than is supported with gradle 4.x
     @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     "rewriteDependencies"("com.puppycrawl.tools:checkstyle:9.3")
     "rewriteDependencies"("com.fasterxml.jackson.module:jackson-module-kotlin:latest.release")
 
-    implementation(platform("org.openrewrite:rewrite-bom:8.6.2"))
+    implementation(platform("org.openrewrite:rewrite-bom:$latest"))
     compileOnly("org.openrewrite:rewrite-core")
     compileOnly("org.openrewrite:rewrite-gradle")
-    compileOnly("org.openrewrite.gradle.tooling:model:1.3.1")
+    compileOnly("org.openrewrite.gradle.tooling:model:$latest")
     compileOnly("org.openrewrite:rewrite-groovy")
     compileOnly("org.openrewrite:rewrite-hcl")
     compileOnly("org.openrewrite:rewrite-java")
     compileOnly("org.openrewrite:rewrite-json")
-    compileOnly("org.openrewrite:rewrite-kotlin:1.4.11")
+    compileOnly("org.openrewrite:rewrite-kotlin:$latest")
     compileOnly("org.openrewrite:rewrite-properties")
     compileOnly("org.openrewrite:rewrite-protobuf")
     compileOnly("org.openrewrite:rewrite-xml")
     compileOnly("org.openrewrite:rewrite-yaml")
-    compileOnly("org.openrewrite:rewrite-polyglot:1.6.1")
+    compileOnly("org.openrewrite:rewrite-polyglot:$latest")
     @Suppress("VulnerableLibrariesLocal", "RedundantSuppression")
     compileOnly("com.puppycrawl.tools:checkstyle:9.3")
     compileOnly("org.jetbrains.kotlin:kotlin-gradle-plugin:latest.release")

From 5e7be11f8dbf48ff5289daffbcca2f64b008e5b4 Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Fri, 29 Sep 2023 17:00:37 -0700
Subject: [PATCH 15/20] Update kotlin version

---
 plugin/build.gradle.kts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/build.gradle.kts b/plugin/build.gradle.kts
index 003ddf497..845263de0 100644
--- a/plugin/build.gradle.kts
+++ b/plugin/build.gradle.kts
@@ -7,7 +7,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import java.util.*
 
 plugins {
-    kotlin("jvm") version("1.8.0")
+    kotlin("jvm") version("1.9.0")
     id("com.gradle.plugin-publish") version "1.1.0"
     id("com.github.hierynomus.license") version "0.16.1"
 }

From bd6372d0df6ae435fe07ab0bfbaa1ad9c11d0174 Mon Sep 17 00:00:00 2001
From: Wesley R <wesleyrogers01@gmail.com>
Date: Tue, 10 Oct 2023 13:51:12 -0400
Subject: [PATCH 16/20] fix: use separate rewrite-polyglot version (#233)
 (#235)

This commit fixes issue #233, where specifying a
rewriteVersion inside the rewrite configuration block
would result in rewrite-polyglot failing to resolve
to a proper version.

Co-authored-by: Wesley Rogers <wesley.rogers@sas.com>
---
 .../gradle/DefaultRewriteExtension.java       |  5 +-
 .../gradle/RewriteResolveDependenciesTest.kt  | 55 +++++++++++++++++++
 2 files changed, 58 insertions(+), 2 deletions(-)
 create mode 100644 plugin/src/test/kotlin/org/openrewrite/gradle/RewriteResolveDependenciesTest.kt

diff --git a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
index a8856d872..2ae0f78f5 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/DefaultRewriteExtension.java
@@ -217,12 +217,13 @@ public String getRewriteVersion() {
         return rewriteVersion;
     }
 
+    private String rewritePolyglotVersion;
     @Override
     public String getRewritePolyglotVersion() {
-        if (rewriteVersion == null) {
+        if (rewritePolyglotVersion == null) {
             return getVersionProps().getProperty("org.openrewrite:rewrite-polyglot");
         }
-        return rewriteVersion;
+        return rewritePolyglotVersion;
     }
 
     private String rewriteGradleModelVersion;
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteResolveDependenciesTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteResolveDependenciesTest.kt
new file mode 100644
index 000000000..d18446ad3
--- /dev/null
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteResolveDependenciesTest.kt
@@ -0,0 +1,55 @@
+/*
+ * Copyright ${year} the original author or authors.
+ * <p>
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * <p>
+ * https://www.apache.org/licenses/LICENSE-2.0
+ * <p>
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.openrewrite.gradle
+
+import org.assertj.core.api.Assertions.assertThat
+import org.gradle.testkit.runner.TaskOutcome
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+import java.io.File
+
+class RewriteResolveDependenciesTest : RewritePluginTest {
+    @Test
+    fun `Specifying a rewriteVersion does not cause build failures`(
+            @TempDir projectDir: File
+    ) {
+        gradleProject(projectDir) {
+            buildGradle("""
+                plugins {
+                    id("java")
+                    id("org.openrewrite.rewrite")
+                }
+                
+                repositories {
+                    mavenLocal()
+                    mavenCentral()
+                    maven {
+                       url = uri("https://oss.sonatype.org/content/repositories/snapshots")
+                    }
+                }
+                
+                rewrite {
+                    rewriteVersion = "8.6.1"
+                }
+            """)
+        }
+
+        val result = runGradle(projectDir, "rewriteResolveDependencies")
+        val rewriteDryRunResult = result.task(":rewriteResolveDependencies")!!
+        assertThat(rewriteDryRunResult.outcome).isEqualTo(TaskOutcome.SUCCESS)
+    }
+
+}

From cd3fbd12f37edba244c6645a8a210a6b76469e4b Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Thu, 26 Oct 2023 20:48:52 -0700
Subject: [PATCH 17/20] Fix exclusion of whole project directories, allow "**/"
 patterns to match files in the root project

---
 .../gradle/isolated/DefaultProjectParser.java | 56 +++++++++++--------
 1 file changed, 33 insertions(+), 23 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 5c493c5f3..b2fab6f2a 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -80,6 +80,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.function.Consumer;
@@ -614,7 +615,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
             Collection<PathMatcher> exclusions = extension.getExclusions().stream()
                     .map(pattern -> subproject.getProjectDir().toPath().getFileSystem().getPathMatcher("glob:" + pattern))
                     .collect(toList());
-            if (isExcluded(exclusions, subproject.getProjectDir().toPath())) {
+            if (isExcluded(exclusions, baseDir.relativize(subproject.getProjectDir().toPath()))) {
                 logger.lifecycle("Skipping project {} because it is excluded", subproject.getPath());
                 return Stream.empty();
             }
@@ -909,31 +910,35 @@ private SourceFileStream parseGradleFiles(
                 if (gradleParser == null) {
                     gradleParser = gradleParser();
                 }
-                sourceFiles = Stream.concat(
-                        sourceFiles,
-                        gradleParser
-                                .parse(singleton(settingsGradleFile.toPath()), baseDir, ctx)
-                                .map(sourceFile -> {
-                                    if (finalGs == null) {
-                                        return sourceFile;
-                                    }
-                                    return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
-                                }));
-                gradleFileCount++;
+                if(!isExcluded(exclusions, settingsPath)) {
+                    sourceFiles = Stream.concat(
+                            sourceFiles,
+                            gradleParser
+                                    .parse(singleton(settingsGradleFile.toPath()), baseDir, ctx)
+                                    .map(sourceFile -> {
+                                        if (finalGs == null) {
+                                            return sourceFile;
+                                        }
+                                        return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
+                                    }));
+                    gradleFileCount++;
+                }
                 alreadyParsed.add(settingsGradleFile.toPath());
             } else if (settingsGradleKtsFile.exists()) {
                 Path settingsPath = baseDir.relativize(settingsGradleKtsFile.toPath());
-                sourceFiles = Stream.concat(
-                        sourceFiles,
-                        PlainTextParser.builder().build()
-                                .parse(singleton(settingsGradleKtsFile.toPath()), baseDir, ctx)
-                                .map(sourceFile -> {
-                                    if (finalGs == null) {
-                                        return sourceFile;
-                                    }
-                                    return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
-                                }));
-                gradleFileCount++;
+                if(!isExcluded(exclusions, settingsPath)) {
+                    sourceFiles = Stream.concat(
+                            sourceFiles,
+                            PlainTextParser.builder().build()
+                                    .parse(singleton(settingsGradleKtsFile.toPath()), baseDir, ctx)
+                                    .map(sourceFile -> {
+                                        if (finalGs == null) {
+                                            return sourceFile;
+                                        }
+                                        return sourceFile.withMarkers(sourceFile.getMarkers().add(finalGs));
+                                    }));
+                    gradleFileCount++;
+                }
                 alreadyParsed.add(settingsGradleKtsFile.toPath());
             }
         }
@@ -1099,6 +1104,11 @@ private boolean isExcluded(Collection<PathMatcher> exclusions, Path path) {
                 return true;
             }
         }
+        // PathMather will not evaluate the path "build.gradle" to be matched by the pattern "**/build.gradle"
+        // This is counter-intuitive for most users and would otherwise require separate exclusions for files at the root and files in subdirectories
+        if(!path.isAbsolute() && !path.startsWith(File.separator)) {
+            return isExcluded(exclusions, Paths.get("/" + path));
+        }
         return false;
     }
 

From 0daa455128fe26ab97e1754adc23e1b55b931445 Mon Sep 17 00:00:00 2001
From: Kun Li <122563761+kunli2@users.noreply.github.com>
Date: Fri, 27 Oct 2023 08:45:21 -0700
Subject: [PATCH 18/20] exclude parse kotlin files under path
 protos/build/generated (#237)

---
 .../org/openrewrite/gradle/isolated/DefaultProjectParser.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index b2fab6f2a..e66388f16 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -739,7 +739,9 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                 }
 
                 if (subproject.getPlugins().hasPlugin("org.jetbrains.kotlin.jvm")) {
+                    String excludedProtosPath = subproject.getProjectDir().getPath() + "/protos/build/generated";
                     List<Path> kotlinPaths = unparsedSources.stream()
+                            .filter(it -> !it.toString().startsWith(excludedProtosPath))
                             .filter(it -> it.toString().endsWith(".kt"))
                             .collect(toList());
 

From c4d0ef275d971ea9d4a2c0e9390b6e73d5e8d6d5 Mon Sep 17 00:00:00 2001
From: traceyyoshima <tracey.yoshima@gmail.com>
Date: Fri, 17 Nov 2023 12:36:14 -0700
Subject: [PATCH 19/20] Fix: parse all sort sets in
 parseMultiplatformKotlinProject.

---
 .../org/openrewrite/gradle/isolated/DefaultProjectParser.java    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index e66388f16..27f1f8a60 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -1080,7 +1080,6 @@ private SourceFileStream parseMultiplatformKotlinProject(Project subproject, Col
                     sourceFileStream = sourceFileStream.concat(cus.map(addProvenance(sourceSetProvenance)), kotlinPaths.size());
                     logger.info("Scanned {} Kotlin sources in {}/{}", kotlinPaths.size(), subproject.getPath(), kotlinDirectorySet.getName());
                 }
-                return sourceFileStream;
             } catch (Exception e) {
                 logger.warn("Failed to resolve sourceSet from {}:{}. Some type information may be incomplete",
                         subproject.getPath(), sourceSetName);

From fdfd1aed8ebc297614a445d413222c3792f2ad11 Mon Sep 17 00:00:00 2001
From: Sam Snyder <sam@moderne.io>
Date: Mon, 20 Nov 2023 13:47:58 -0800
Subject: [PATCH 20/20] Add test covering settings defined repositories

---
 .../gradle/isolated/DefaultProjectParser.java |  3 +-
 .../openrewrite/gradle/GradleProjectSpec.kt   | 84 +++++++++----------
 .../openrewrite/gradle/RewritePluginTest.kt   |  7 +-
 .../org/openrewrite/gradle/RewriteRunTest.kt  | 80 ++++++++++++++++--
 4 files changed, 121 insertions(+), 53 deletions(-)

diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 27f1f8a60..eee2b7b14 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -888,12 +888,11 @@ private SourceFileStream parseGradleFiles(
                 if (buildScriptPath.toString().endsWith(".gradle")) {
                     gradleParser = gradleParser();
                     sourceFiles = gradleParser.parse(singleton(buildGradleFile.toPath()), baseDir, ctx);
-                    gradleFileCount++;
                 } else {
                     sourceFiles = PlainTextParser.builder().build()
                             .parse(singleton(buildGradleFile.toPath()), baseDir, ctx);
-                    gradleFileCount++;
                 }
+                gradleFileCount++;
                 sourceFiles = sourceFiles.map(sourceFile -> sourceFile.withMarkers(sourceFile.getMarkers().add(gp)));
                 alreadyParsed.add(project.getBuildscript().getSourceFile().toPath());
             }
diff --git a/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt b/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
index 6b147d45e..92620ec2f 100644
--- a/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
+++ b/plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt
@@ -22,10 +22,10 @@ import java.io.File
  * Utility to help with writing gradle projects to disk to assist with plugin testing
  */
 class GradleProjectSpec(
-    val dir: File
+    private val dir: File
 ) {
-    val subprojects: MutableList<GradleProjectSpec> = mutableListOf()
-    val sourceSets: MutableList<GradleSourceSetSpec> = mutableListOf()
+    private val subprojects: MutableList<GradleProjectSpec> = mutableListOf()
+    private val sourceSets: MutableList<GradleSourceSetSpec> = mutableListOf()
 
     @Language("groovy")
     var groovyBuildScript: String? = null
@@ -37,7 +37,7 @@ class GradleProjectSpec(
     @Language("groovy")
     var settingsGradle: String? = null
     fun settingsGradle(@Language("groovy") text: String) {
-        settingsGradle = text.trimIndent();
+        settingsGradle = text.trimIndent()
     }
 
     @Language("yaml")
@@ -52,12 +52,12 @@ class GradleProjectSpec(
         checkstyleXml = text.trimIndent()
     }
 
-    val propertiesFiles: MutableMap<String, String> = mutableMapOf()
+    private val propertiesFiles: MutableMap<String, String> = mutableMapOf()
     fun propertiesFile(name: String, @Language("properties") text: String) {
         propertiesFiles[name] = text
     }
 
-    val textFiles: MutableMap<String, String> = mutableMapOf()
+    private val textFiles: MutableMap<String, String> = mutableMapOf()
     fun textFile(name: String, text: String) {
         textFiles[name] = text
     }
@@ -77,8 +77,17 @@ class GradleProjectSpec(
     fun build(): GradleProjectSpec {
         dir.mkdirs()
 
-        if (settingsGradle != null) {
-            File(dir, "settings.gradle").writeText(settingsGradle!!)
+        val settings = File(dir, "settings.gradle")
+        if(settingsGradle == null) {
+            val settingsText = "rootProject.name = \"${dir.name}\"\n"
+            if (subprojects.isEmpty()) {
+                settings.writeText("rootProject.name = \"${dir.name}\"\n")
+            } else {
+                val subprojectsDeclarations = subprojects.joinToString("\n") { subproject  ->  "include('${subproject.dir.name}')" }
+                settings.writeText(settingsText + subprojectsDeclarations)
+            }
+        } else {
+            settings.writeText(settingsGradle!!)
         }
 
         if (groovyBuildScript != null) {
@@ -90,21 +99,21 @@ class GradleProjectSpec(
         }
 
         if (checkstyleXml != null) {
-            File(dir, "config/checkstyle/checkstyle.xml").apply{ 
+            File(dir, "config/checkstyle/checkstyle.xml").apply{
                 parentFile.mkdirs()
                 writeText(checkstyleXml!!)
             }
         }
 
         for (props in propertiesFiles.entries) {
-            File(dir, props.key).apply{ 
+            File(dir, props.key).apply{
                 parentFile.mkdirs()
                 writeText(props.value)
             }
         }
 
         for (text in textFiles.entries) {
-            File(dir, text.key).apply{ 
+            File(dir, text.key).apply{
                 parentFile.mkdirs()
                 writeText(text.value)
             }
@@ -113,46 +122,37 @@ class GradleProjectSpec(
         for (sourceSet in sourceSets) {
             sourceSet.build(File(dir, "src"))
         }
-
-        val settings = File(dir, "settings.gradle")
-        val settingsText = "rootProject.name = \"${dir.name}\"\n"
-        if (subprojects.isEmpty()) {
-            settings.writeText("rootProject.name = \"${dir.name}\"\n")
-        } else {
-            val subprojectsDeclarations = subprojects.joinToString("\n") { subproject  ->  "include('${subproject.dir.name}')" }
-            settings.writeText(settingsText + subprojectsDeclarations)
-            for (subproject in subprojects) {
-                subproject.build()
-            }
+        for (subproject in subprojects) {
+            subproject.build()
         }
         return this
     }
 }
 
 class GradleSourceSetSpec(
-    val name: String
+    private val name: String
 ) {
-    val javaSources: MutableList<String> = mutableListOf()
+    private val javaSources: MutableList<String> = mutableListOf()
     fun java(@Language("java") source: String) {
         javaSources.add(source.trimIndent())
     }
 
-    val kotlinSources: MutableList<String> = mutableListOf()
+    private val kotlinSources: MutableList<String> = mutableListOf()
     fun kotlin(@Language("kotlin") source: String) {
         kotlinSources.add(source.trimIndent())
     }
 
-    val propertiesFiles: MutableMap<String, String> = mutableMapOf()
+    private val propertiesFiles: MutableMap<String, String> = mutableMapOf()
     fun propertiesFile(name: String, @Language("properties") text: String) {
         propertiesFiles[name] = text
     }
 
-    val yamlFiles: MutableMap<String, String> = mutableMapOf()
+    private val yamlFiles: MutableMap<String, String> = mutableMapOf()
     fun yamlFile(name: String, @Language("yaml") text: String) {
         yamlFiles[name] = text
     }
 
-    val groovyClasses: MutableList<String> = mutableListOf()
+    private val groovyClasses: MutableList<String> = mutableListOf()
     fun groovyClass(@Language("groovy") source: String) {
         groovyClasses.add(source.trimIndent())
     }
@@ -162,7 +162,7 @@ class GradleSourceSetSpec(
     fun build(dir: File): GradleSourceSetSpec {
         dir.mkdirs()
         for (javaSource in javaSources) {
-            val peckage = if (javaSource.startsWith("package")) {
+            val packageDecl = if (javaSource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+);".toRegex(RegexOption.MULTILINE)
                     .find(javaSource)!!
                     .groupValues[1]
@@ -170,18 +170,18 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(javaSource)!!.groupValues[2]
-            val path = if (peckage.isEmpty()) {
+            val path = if (packageDecl.isEmpty()) {
                 "$name/java/$clazz.java"
             } else {
-                "$name/java/$peckage/$clazz.java"
+                "$name/java/$packageDecl/$clazz.java"
             }
-            File(dir, path).apply{ 
+            File(dir, path).apply{
                 parentFile.mkdirs()
                 writeText(javaSource)
             }
         }
         for (kotlinSource in kotlinSources) {
-            val peckage = if (kotlinSource.startsWith("package")) {
+            val packageDecl = if (kotlinSource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+)".toRegex(RegexOption.MULTILINE)
                     .find(kotlinSource)!!
                     .groupValues[1]
@@ -189,18 +189,18 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(kotlinSource)!!.groupValues[2]
-            val path = if (peckage.isEmpty()) {
+            val path = if (packageDecl.isEmpty()) {
                 "$name/kotlin/$clazz.kt"
             } else {
-                "$name/kotlin/$peckage/$clazz.kt"
+                "$name/kotlin/$packageDecl/$clazz.kt"
             }
-            File(dir, path).apply{ 
+            File(dir, path).apply{
                 parentFile.mkdirs()
                 writeText(kotlinSource)
             }
         }
         for (groovySource in groovyClasses) {
-            val peckage = if (groovySource.startsWith("package")) {
+            val packageDecl = if (groovySource.startsWith("package")) {
                 "package\\s+([a-zA-Z0-9.]+);?".toRegex(RegexOption.MULTILINE)
                     .find(groovySource)!!
                     .groupValues[1]
@@ -208,19 +208,19 @@ class GradleSourceSetSpec(
                 ""
             }.replace(".", "/")
             val clazz = ".*(class|interface|enum)\\s+([a-zA-Z0-9-_]+)".toRegex(RegexOption.MULTILINE).find(groovySource)!!.groupValues[2]
-            val path = if (peckage.isEmpty()) {
+            val path = if (packageDecl.isEmpty()) {
                 "$name/groovy/$clazz.groovy"
             } else {
-                "$name/groovy/$peckage/$clazz.groovy"
+                "$name/groovy/$packageDecl/$clazz.groovy"
             }
-            File(dir, path).apply{ 
+            File(dir, path).apply{
                 parentFile.mkdirs()
                 writeText(groovySource)
             }
         }
         if (propertiesFiles.isNotEmpty()) {
             for (props in propertiesFiles.entries) {
-                File(dir, "$name/resources/${props.key}").apply{ 
+                File(dir, "$name/resources/${props.key}").apply{
                     parentFile.mkdirs()
                     writeText(props.value)
                 }
@@ -228,7 +228,7 @@ class GradleSourceSetSpec(
         }
         if (yamlFiles.isNotEmpty()) {
             for (yaml in yamlFiles.entries) {
-                File(dir, "$name/resources/${yaml.key}").apply{ 
+                File(dir, "$name/resources/${yaml.key}").apply{
                     parentFile.mkdirs()
                     writeText(yaml.value)
                 }
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
index d2b7f9e9b..d149186c5 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewritePluginTest.kt
@@ -29,7 +29,7 @@ interface RewritePluginTest {
         GradleRunner.create()
             .withDebug(ManagementFactory.getRuntimeMXBean().inputArguments.toString().indexOf("-agentlib:jdwp") > 0)
             .withProjectDir(testDir)
-            .apply{ 
+            .apply{
                 if (gradleVersion != null) {
                     withGradleVersion(gradleVersion)
                 }
@@ -44,4 +44,9 @@ interface RewritePluginTest {
         val currentVersion = if (gradleVersion == null) GradleVersion.current() else GradleVersion.version(gradleVersion)
         return currentVersion < GradleVersion.version("6.1")
     }
+
+    fun lessThanGradle6_8(): Boolean {
+        val currentVersion = if (gradleVersion == null) GradleVersion.current() else GradleVersion.version(gradleVersion)
+        return currentVersion < GradleVersion.version("6.8")
+    }
 }
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index 8aee56aaa..4ba59e8d8 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -21,7 +21,6 @@ package org.openrewrite.gradle
 
 import org.assertj.core.api.Assertions.assertThat
 import org.gradle.testkit.runner.TaskOutcome
-import org.junit.jupiter.api.Disabled
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.condition.DisabledIf
 import org.junit.jupiter.api.condition.DisabledOnOs
@@ -446,8 +445,8 @@ class RewriteRunTest : RewritePluginTest {
             rewriteYaml("""
                 type: specs.openrewrite.org/v1beta/recipe
                 name: org.openrewrite.test.RemoveJacksonCore
-                displayName: Rename build.gradle to build.gradle.kts
-                description: Rename build.gradle to build.gradle.kts
+                displayName: Remove jackson-core
+                description: Remove jackson-core
                 recipeList:
                   - org.openrewrite.gradle.RemoveDependency:
                       groupId: com.fasterxml.jackson.core
@@ -516,6 +515,73 @@ class RewriteRunTest : RewritePluginTest {
             """.trimIndent())
     }
 
+
+    @DisabledIf("lessThanGradle6_8")
+    @Test
+    fun dependencyRepositoriesDeclaredInSettings(
+        @TempDir projectDir: File
+    ) {
+        gradleProject(projectDir) {
+            rewriteYaml("""
+                type: specs.openrewrite.org/v1beta/recipe
+                name: org.openrewrite.test.UpgradeJacksonCore
+                displayName: Remove jackson-core
+                description: Remove jackson-core
+                recipeList:
+                  - org.openrewrite.gradle.UpgradeDependencyVersion:
+                      groupId: com.fasterxml.jackson.core
+                      artifactId: jackson-core
+                      nevVersion: 2.16.0
+            """)
+            settingsGradle("""
+                dependencyResolutionManagement {
+                    repositories {
+                        mavenLocal()
+                        mavenCentral()
+                        maven {
+                           url = uri("https://oss.sonatype.org/content/repositories/snapshots")
+                        }
+                    }
+                }
+            """)
+            buildGradle("""
+                plugins {
+                    id("java")
+                    id("org.openrewrite.rewrite")
+                }
+                
+                dependencies {
+                    implementation("com.fasterxml.jackson.core:jackson-core:2.15.1")
+                }
+                
+                rewrite {
+                    activeRecipe("org.openrewrite.test.UpgradeJacksonCore")
+                }
+            """)
+        }
+
+        val result = runGradle(projectDir, "rewriteRun")
+        val rewriteRunResult = result.task(":rewriteRun")!!
+        assertThat(rewriteRunResult.outcome).isEqualTo(TaskOutcome.SUCCESS)
+
+        assertThat(projectDir.resolve("build.gradle").readText())
+            //language=groovy
+            .isEqualTo("""
+                plugins {
+                    id("java")
+                    id("org.openrewrite.rewrite")
+                }
+                
+                dependencies {
+                    implementation("com.fasterxml.jackson.core:jackson-core:2.16.0")
+                }
+                
+                rewrite {
+                    activeRecipe("org.openrewrite.test.UpgradeJacksonCore")
+                }
+                """.trimIndent())
+    }
+
     @Test
     fun mergeConfiguredAndAutodetectedStyles(@TempDir projectDir: File) {
         gradleProject(projectDir) {
@@ -913,7 +979,6 @@ class RewriteRunTest : RewritePluginTest {
             )
     }
 
-    @Disabled("Applicability tests are no longer supported for YAML recipes")
     @DisabledOnOs(OS.WINDOWS) // A file handle I haven't been able to track down is left open, causing JUnit to fail to clean up the directory on Windows
     @Issue("https://github.com/openrewrite/rewrite-gradle-plugin/issues/176")
     @Test
@@ -937,10 +1002,9 @@ class RewriteRunTest : RewritePluginTest {
                         name: com.example.TextToSam
                         displayName: Changes contents of sam.txt
                         description: Change contents of sam.txt to "sam"
-                        applicability:
-                          singleSource:
-                            - org.openrewrite.FindSourceFiles:
-                                filePattern: "**/sam.txt"
+                        preconditions:
+                          - org.openrewrite.FindSourceFiles:
+                              filePattern: "**/sam.txt"
                         recipeList:
                           - org.openrewrite.text.ChangeText:
                               toText: sam