diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..151a76d7
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,12 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-case-conflict
+    -   id: check-toml
diff --git a/source/docs/extensions/index.md b/source/docs/extensions/index.md
index 915d46bd..a77fe88d 100644
--- a/source/docs/extensions/index.md
+++ b/source/docs/extensions/index.md
@@ -1 +1,3 @@
-(extensions)=
\ No newline at end of file
+(extensions)=
+
+# Extensions
diff --git a/source/docs/index.md b/source/docs/index.md
index 33e7b46c..8ba3addd 100644
--- a/source/docs/index.md
+++ b/source/docs/index.md
@@ -1,6 +1,6 @@
 (docs)=
 
-# Welcome 
+# Guide
 
 Avogadro is a free, open-source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.
 
@@ -24,18 +24,18 @@ This is a tip – something that can help you work better
 
 This book would not be possible without the help and effort of many people, including Avogadro developers, translators, and users world-wide.
 
-Funding for the Avogadro manual was provided by the [University of Pittsburgh Department of Chemistry](http://www.chem.pitt.edu/).
+Initial funding for the Avogadro manual was provided by the [University of Pittsburgh Department of Chemistry](http://www.chem.pitt.edu/).
 
 * Version 1 - Summer 2015 - Taylor Cornell and Geoffrey Hutchison
-* Version 2 - Summer 2022/2023 - Geoffrey Hutchison
+* Version 2 - 2022-204 - Geoffrey Hutchison
 
 ```{toctree}
 ---
 hidden: true
-caption: Welcome
+caption: User Documentation
 ---
 
-self
+Introduction <self>
 whats-new-in-avogadro-2/index
 getting-started/index
 tools/index
diff --git a/source/docs/tools/draw-tool.md b/source/docs/tools/draw-tool.md
index c6c440b7..16f7b25b 100644
--- a/source/docs/tools/draw-tool.md
+++ b/source/docs/tools/draw-tool.md
@@ -5,7 +5,7 @@
 Molecules are built and edited with the Draw Tool, which allows "free-hand" sketching of new molecules.
 
 ```{tip} **New in 2.0**
-You can also use the new [Template Tool](tools-template-tool), which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes.
+You can also use the new [Template Tool](template-tool), which makes it quicker and easier to attach functional groups or assemble inorganic/organometallic complexes.
 ```
 
 ![Screenshot of the draw tool](../../_static/draw-tool.png)
diff --git a/source/docs/tools/index.md b/source/docs/tools/index.md
index 0104f541..1d53f116 100644
--- a/source/docs/tools/index.md
+++ b/source/docs/tools/index.md
@@ -13,6 +13,7 @@ After selecting a tool, the name of the tool and any options available for the t
 ```{toctree}
 ---
 caption: Tools
+maxdepth: 1
 ---
 
 navigation-tool
@@ -25,4 +26,4 @@ bond-centric-manipulation-tool
 measure-tool
 animation-tool
 align-tool
-```
\ No newline at end of file
+```