docs: rename INDEX files to meaningful names and fix navigation

- Renamed subdirectory INDEX.md files to section-specific names:
  - user/INDEX.md → user/user-guide.md
  - developer/INDEX.md → developer/development.md
  - operations/INDEX.md → operations/operations.md
  - contributing/INDEX.md → contributing/contributing.md
  - developer/api/INDEX.md → developer/api/api-reference.md
  - developer/api/collections/INDEX.md → developer/api/collections/collections-api.md

- Updated all internal links to use new filenames
- Updated navigation.go to skip subdirectory INDEX files from sidebar
- Added Dockerfile to include docs directory in container build

This fixes the issue where multiple 'INDEX' links appeared in the sidebar,
making navigation confusing. Now each section has a descriptive name.

docs/developer/api/collections/collections-api.md

@@ -0,0 +1,35 @@
+# Collections API
+
+See [Collections API](../../collections-api.md) for complete collections documentation.
+
+## Quick Links
+
+- [List Collections](list_collections.md) - Get all collections
+- [Get Collection](get_collection.md) - Get collection details
+- [Create Collection](create_collection.md) - Create a new collection
+- [Update Collection](update_collection.md) - Update collection metadata
+- [Delete Collection](delete_collection.md) - Delete a collection
+- [Add Auto-Assign Rule](add_auto_assign_rule.md) - Add automatic book assignment rule
+- [Remove Auto-Assign Rule](remove_auto_assign_rule.md) - Remove assignment rule
+- [Test Rule](test_rule.md) - Test assignment rule
+- [Bulk Assign](bulk_assign.md) - Bulk assign books to collection
+- [Create Shelf Mapping](create_shelf_mapping.md) - Map collection to device shelf
+- [Delete Shelf Mapping](delete_shelf_mapping.md) - Remove shelf mapping
+
+---
+
+## Overview
+
+Collections allow you to organize your books into custom groups with automatic assignment rules.
+
+## Features
+
+- **Manual Assignment**: Add specific books to collections
+- **Auto-Assignment**: Define rules to automatically assign books based on metadata
+- **Device Sync**: Collections sync as shelves on Kobo/KOReader devices
+- **Flexible Rules**: Filter by genre, series, tags, and more
+
+## See Also
+
+- [Collections API](../../collections-api.md) - Complete API reference
+- [Sync Guide](../../user/sync-guide.md) - How collections sync to devices