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/development.md

@@ -0,0 +1,77 @@
+# Developer Documentation
+
+Welcome to the Bookhoard developer documentation. This section contains API references, protocol specifications, and technical documentation for integrating with Bookhoard.
+
+## 📚 API Documentation
+
+### Complete API Reference
+
+- **[API Reference](api-reference.md)** - Complete REST API reference
+  - Authentication
+  - User management
+  - Libraries
+  - Media items
+  - Reading progress
+  - Notes & highlights
+  - Analytics
+  - Book matching
+  - OPDS
+  - Sync protocols (KOReader, Kobo)
+  - WebSocket
+
+### Split Endpoint Documentation
+
+Browse individual endpoint documentation with interactive API Explorer:
+
+- **[API Documentation](api/INDEX.md)** - Split endpoint docs
+  - [Authentication](api/authentication/) - Register, login, tokens
+  - [Users](api/users/) - Profile management
+  - [Libraries](api/libraries/) - Library operations
+  - [Media Items](api/media-items/) - Book/ebook management
+  - [Progress](api/progress/) - Reading progress tracking
+  - [Notes](api/notes/) - User notes
+  - [Highlights](api/highlights/) - Book highlights
+  - [Ratings](api/ratings/) - Book ratings
+  - [Devices](api/devices/) - Device management
+  - [Analytics](api/analytics/) - Usage statistics
+  - [Book Matching](api/book-matching/) - Search and link books
+  - [Collections](api/collections/) - Collection management
+  - [OPDS](api/opds/) - Open Publication Distribution
+  - [Sync Protocols](api/sync/) - KOReader and Kobo sync
+  - [WebSocket](api/websocket/) - Real-time events
+
+### Collections API
+
+- **[Collections API](collections-api.md)** - Complete collections API reference
+  - Create and manage collections
+  - Auto-assign rules
+  - Test rules
+  - Bulk operations
+  - Device shelf mappings
+
+## 🔌 Protocol Specifications
+
+### Sync Protocols
+
+- **[Kobo Sync Protocol](api/sync/kobo-protocol.md)** - Kobo device sync protocol
+  - Kobo markup sync
+  - Library fetch
+  - Authentication
+
+- **[KOReader Sync Protocol](api/sync/koreader-protocol.md)** - KOReader sync protocol
+  - Progress sync
+  - Metadata fetch
+  - Conflict handling
+
+### WebSocket Protocol
+
+- **[WebSocket API](websocket-api.md)** - Real-time sync and events
+  - Connection flow
+  - Message format
+  - Event types
+  - Authentication
+
+---
+
+**Looking for user documentation?** See the [User Portal](../user/INDEX.md)
+**Need to deploy?** See the [Operations Portal](../operations/INDEX.md)