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/api-reference.md

@@ -0,0 +1,79 @@
+# API Documentation
+
+Complete reference for Bookhoard REST API endpoints.
+
+## Quick Links
+
+- [Authentication](authentication/) - User registration, login, tokens
+- [Users](users/) - Profile management
+- [Libraries](libraries/) - Library management
+- [Media Items](media-items/) - Book/ebook operations
+- [Progress](progress/) - Reading progress tracking
+- [Notes](notes/) - User notes management
+- [Highlights](highlights/) - Book highlights
+- [Ratings](ratings/) - Book ratings
+- [Devices](devices/) - Device registration and sync
+- [Analytics](analytics/) - Usage statistics
+- [Book Matching](book-matching/) - Search and link books
+- [Collections](collections/) - See [Collections API](../collections-api.md)
+- [OPDS](opds/) - Open Publication Distribution
+- [Sync Protocols](sync/) - KOReader and Kobo sync
+- [WebSocket](websocket/) - Real-time sync events
+
+---
+
+## Authentication
+
+See [Authentication Endpoints](authentication/)
+
+## Users & Profiles
+
+See [User Management](users/)
+
+## Libraries
+
+See [Library Management](libraries/)
+
+## Media Items
+
+See [Media Item Operations](media-items/)
+
+## Reading Progress
+
+See [Progress Tracking](progress/)
+
+## Notes & Highlights
+
+See [Notes Management](notes/) and [Highlights Management](highlights/)
+
+## Ratings
+
+See [Ratings System](ratings/)
+
+## Device Management
+
+See [Device Registration & Sync](devices/)
+
+## Analytics
+
+See [Usage Analytics](analytics/)
+
+## Book Matching & Linking
+
+See [Book Matching](book-matching/)
+
+## Collections
+
+See [Collections API](../collections-api.md) or [Collections Endpoints](collections/)
+
+## OPDS
+
+See [OPDS Feeds](opds/)
+
+## Sync Protocols
+
+See [KOReader Sync](sync/) and [Kobo Sync](sync/)
+
+## WebSocket
+
+See [WebSocket Protocol](websocket/)