Remove duplicate 'Architecture Topics' listings in Sphinx docs

- Remove 'Available Topics' section from architecture/index.md generation
- Use toctree with caption instead of manual topic list
- Simplify index.md sidebar hierarchy to avoid duplication
- toctree now serves as single source of truth for topic navigation

Author: jmchilton

doc/source/architecture/dependencies.md

@@ -12,10 +12,6 @@
 - Understand JavaScript dependency management
 - Learn about the wheels server
 
-## Dependencies
-
-
-
 ## Dependencies - Python
 
 `script/common_startup.sh` sets up a `virtualenv` with required dependencies in `$GALAXY_ROOT/.venv` (or `$GALAXY_VIRTUAL_ENV` if set).

doc/source/architecture/index.md

@@ -4,6 +4,7 @@ Core documentation about Galaxy's internal architecture and design.
 
 ```{toctree}
 :maxdepth: 1
+:caption: Architecture Topics
 
 ecosystem
 project-management
@@ -19,21 +20,3 @@ dependencies
 startup
 production
 ```
-
-## Available Topics
-
-This section documents Galaxy's key architectural patterns:
-
-- **[Galaxy Ecosystem and Projects](ecosystem.md)**
-- **[Galaxy Project Management and Contribution](project-management.md)**
-- **[Galaxy Architecture Principles](principles.md)**
-- **[Galaxy Files and Directory Structure](files.md)**
-- **[Galaxy Web Frameworks](frameworks.md)**
-- **[Dependency Injection in Galaxy](dependency-injection.md)**
-- **[Galaxy Task Management with Celery](tasks.md)**
-- **[Galaxy Application Components: Models, Managers, and Services](application-components.md)**
-- **[Galaxy Plugin Architecture](plugins.md)**
-- **[Galaxy Client Architecture](client.md)**
-- **[Galaxy Dependencies Management](dependencies.md)**
-- **[Galaxy Startup Process](startup.md)**
-- **[Galaxy Production Deployment](production.md)**

doc/source/architecture/production.md

@@ -13,10 +13,6 @@
 - Understand multi-process and multi-host setups
 - Learn about usegalaxy.org infrastructure
 
-## Production Galaxy - usegalaxy.org
-
-
-
 #### Default
 
 SQLite

doc/source/architecture/startup.md

@@ -13,10 +13,6 @@
 - Understand dependency installation
 - Learn about database migrations and plugin loading
 
-## Galaxy Startup Process
-
-
-
 ## Cloning Galaxy
 
 ```bash

doc/source/index.md

@@ -4,7 +4,6 @@ This section documents Galaxy's internal architecture and design patterns.
 
 ```{toctree}
 :maxdepth: 2
-:caption: Architecture Topics
 
 architecture/index
 ```

outputs/sphinx-docs/build.py

@@ -485,22 +485,12 @@ def update_architecture_index(topics_to_include: list[str]) -> None:
 
 ```{{toctree}}
 :maxdepth: 1
+:caption: Architecture Topics
 
 {toctree_items}
 ```
-
-## Available Topics
-
-This section documents Galaxy's key architectural patterns:
-
 """
 
-    # Add links for each topic in order
-    for topic_id in ordered_topics:
-        if topic_id in topic_metadata:
-            metadata = topic_metadata[topic_id]
-            content += f"- **[{metadata.title}]({topic_id}.md)**\n"
-
     index_file.write_text(content)
     print(f"✓ Updated: {index_file}")