docs(api): complete backend documentation with all missing endpoints

Complete API documentation audit covering all backend endpoints.

Auth Endpoints:
- Fixed endpoint paths from /api/users/me/* to /api/auth/*
- Added update_email.md and update_username.md

Device Management:
- Device shelf operations (add, get, remove, clear)
- Device CRUD operations (update, delete)
- Registration management (pending, approve, reject)

Books Operations:
- Bulk delete and bulk update with normalization
- Download endpoint with format-specific headers

Conflict Resolution:
- Complete conflict management (list, get, resolve, delete)
- Bulk operations (bulk resolve, bulk dismiss, dismiss all)

Sync Protocols:
- KOReader: progress, metadata, library, bookmarks
- Kobo: markup, bookmarks, analytics, initialization, server sync

Scanner:
- Enhanced docs with manga/comic support
- Added 148-line comprehensive overview
- All formats documented (ebooks, comics, manga)

WebSocket:
- Comprehensive real-time sync API
- Messages, topics, authentication, examples

Documentation:
- Updated api-reference.md with all 122+ endpoints
- Updated index.md with new categories

Total: 36 new files, 6 modified files, 100% coverage

docs/developer/api/api-reference.md

@@ -6,18 +6,24 @@ Complete reference for Bookhoard REST API endpoints.
 
 - [Authentication](authentication/) - User registration, login, tokens
 - [Users](users/) - Profile management
+- [Admin](admin/) - Admin operations (user management)
 - [Libraries](libraries/) - Library management
+- [Books](books/) - Bulk book operations and downloads
 - [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
+- [Devices](devices/) - Device registration, sync, and shelf management
 - [Analytics](analytics/) - Usage statistics
 - [Book Matching](book-matching/) - Search and link books
 - [Collections](collections/) - See [Collections API](../collections-api.md)
+- [Conflicts](conflicts/) - Sync conflict resolution
+- [Queue](queue/) - Sync queue management
+- [Scanner](scanner/) - Library scanning and watch mode (admin)
 - [OPDS](opds/) - Open Publication Distribution
-- [Sync Protocols](sync/) - KOReader and Kobo sync
+- [KOReader](koreader/) - KOReader sync protocol
+- [Kobo](kobo/) - Kobo sync protocol
 - [WebSocket](websocket/) - Real-time sync events
 
 ---
@@ -26,6 +32,24 @@ Complete reference for Bookhoard REST API endpoints.
 
 See [Authentication Endpoints](authentication/)
 
+- POST /api/auth/register - Register new user
+- POST /api/auth/login - User login
+- POST /api/auth/refresh - Refresh access token
+- POST /api/auth/logout - User logout
+- GET /api/auth/profile - Get user profile
+- PUT /api/auth/profile - Update user profile
+- PUT /api/auth/email - Update user email
+- PUT /api/auth/username - Update username
+- PUT /api/auth/password - Change password
+- PUT /api/auth/theme - Update theme preference
+
+## Admin
+
+See [Admin Operations](admin/)
+
+- GET /api/auth/users - List all users (admin)
+- PUT /api/auth/users/:id/max-devices - Update user device limit (admin)
+
 ## Users & Profiles
 
 See [User Management](users/)
@@ -34,14 +58,65 @@ See [User Management](users/)
 
 See [Library Management](libraries/)
 
+- GET /api/libraries/types - Get library types
+- POST /api/libraries - Create library (admin)
+- GET /api/libraries - List libraries (admin)
+- GET /api/libraries/:id - Get library (admin)
+- PUT /api/libraries/:id - Update library (admin)
+- DELETE /api/libraries/:id - Delete library (admin)
+- POST /api/libraries/:id/folders - Add library folder (admin)
+- GET /api/libraries/:id/folders - Get library folders (admin)
+- DELETE /api/libraries/:id/folders - Delete library folder (admin)
+- GET /api/libraries/:id/stats - Get library statistics (admin)
+- GET /api/libraries/:id/media-items - Get library media items (admin)
+- POST /api/libraries/:id/scan - Scan library (admin)
+- GET /api/libraries/visibility - Get visible libraries
+- POST /api/libraries/visibility - Set library visibility
+
+## Books
+
+See [Book Operations](books/)
+
+- POST /api/books/bulk-delete - Bulk delete books
+- POST /api/books/bulk-update - Bulk update books (tags/contributors with normalization)
+- GET /api/books/:uuid/download - Download book file
+
 ## Media Items
 
 See [Media Item Operations](media-items/)
 
+- GET /api/media-items - List media items
+- GET /api/media-items/filtered - Filter and sort media items
+- GET /api/media-items/:id - Get media item details
+- POST /api/media-items/:id/rating - Create rating
+- GET /api/media-items/:id/rating - Get rating
+- PUT /api/media-items/:id/rating - Update rating
+- DELETE /api/media-items/:id/rating - Delete rating
+- GET /api/media-items/:id/progress - Get reading progress
+- PUT /api/media-items/:id/progress - Update reading progress
+- DELETE /api/media-items/:id/progress - Delete reading progress
+- GET /api/media-items/:id/notes - Get notes
+- POST /api/media-items/:id/notes - Create note
+- GET /api/media-items/:id/notes/:noteId - Get note
+- PUT /api/media-items/:id/notes/:noteId - Update note
+- DELETE /api/media-items/:id/notes/:noteId - Delete note
+- GET /api/media-items/:id/highlights - Get highlights
+- POST /api/media-items/:id/highlights - Create highlight
+- GET /api/media-items/:id/highlights/:highlightId - Get highlight
+- PUT /api/media-items/:id/highlights/:highlightId - Update highlight
+- DELETE /api/media-items/:id/highlights/:highlightId - Delete highlight
+- POST /api/media-items - Create media item (admin)
+- PUT /api/media-items/:id - Update media item (admin)
+- DELETE /api/media-items/:id - Delete media item (admin)
+
 ## Reading Progress
 
 See [Progress Tracking](progress/)
 
+- GET /api/progress/:id - Get universal progress
+- POST /api/progress/:id - Update universal progress
+- GET /api/progress/:id/history - Get progress history
+
 ## Notes & Highlights
 
 See [Notes Management](notes/) and [Highlights Management](highlights/)
@@ -54,26 +129,139 @@ See [Ratings System](ratings/)
 
 See [Device Registration & Sync](devices/)
 
+- POST /api/devices/register - Initiate device registration
+- POST /api/devices/register/status - Check registration status
+- GET /api/devices - List devices
+- GET /api/devices/:id - Get device
+- PUT /api/devices/:id - Update device
+- DELETE /api/devices/:id - Delete device
+- GET /api/devices/pending - List pending registrations (admin)
+- GET /api/devices/approve/:registration_id - Approve registration (admin)
+- POST /api/devices/reject/:registration_id - Reject registration (admin)
+- POST /api/devices/:id/shelves - Add to shelf (Kobo)
+- GET /api/devices/:id/shelves - Get shelf contents
+- DELETE /api/devices/:id/shelves - Remove from shelf
+- DELETE /api/devices/:id/shelves/clear - Clear shelf
+
 ## Analytics
 
 See [Usage Analytics](analytics/)
 
+- GET /api/analytics/reading-stats - Get reading statistics
+- GET /api/analytics/device-usage - Get device usage stats
+- GET /api/analytics/popular-books - Get popular books
+
 ## Book Matching & Linking
 
 See [Book Matching](book-matching/)
 
+- GET /api/media-items/search - Search media items
+- POST /api/sync/books/query - Query books for matching
+- POST /api/devices/:deviceId/sync/link-book - Link book to media item
+- GET /api/devices/:deviceId/sync/unlinked-books - Get unlinked books
+- POST /api/sync/bulk-link-books - Bulk link books
+- POST /api/sync/auto-link-books - Auto-link books
+- GET /api/sync/unlinked-books/:id/suggestions - Get match suggestions
+- GET /api/devices/:id/file-aliases - Get file aliases
+- POST /api/devices/:id/file-aliases - Create file alias
+- PUT /api/devices/:id/file-aliases/:aliasId - Update file alias
+- DELETE /api/devices/:id/file-aliases/:aliasId - Delete file alias
+- GET /api/books/match - Get book matches
+
 ## Collections
 
 See [Collections API](../collections-api.md) or [Collections Endpoints](collections/)
 
+## Conflicts
+
+See [Conflict Resolution](conflicts/)
+
+- GET /api/conflicts - List conflicts
+- GET /api/conflicts/:id - Get conflict details
+- POST /api/conflicts/:id/resolve - Resolve conflict
+- DELETE /api/conflicts/:id - Delete conflict
+- POST /api/conflicts/dismiss-all - Dismiss all resolved
+- POST /api/conflicts/bulk-resolve - Bulk resolve conflicts
+- POST /api/conflicts/bulk-dismiss - Bulk dismiss conflicts
+
+## Queue Management
+
+See [Sync Queue](queue/)
+
+- GET /api/queue/devices/:device_id/stats - Get device queue stats
+- GET /api/queue/devices/:device_id/items - List device queue items
+- POST /api/queue/items/:item_id/retry - Retry queue item
+- DELETE /api/queue/items/:item_id - Delete queue item
+- DELETE /api/queue/devices/:device_id/clear - Clear device queue
+- GET /api/queue/items - List all queue items (admin)
+
+## Scanner (Admin)
+
+See [Scanner Operations](scanner/)
+
+- [Scanner Overview](scanner/overview.md) - Supported formats, metadata extraction, and features
+- POST /api/scanner/scan - One-time library scan (ebooks, manga, comics)
+- POST /api/scanner/start - Start automated scanner
+- POST /api/scanner/stop - Stop automated scanner
+- GET /api/scanner/status/:jobId - Get scan job status
+- POST /api/scanner/watch/start - Start watch mode (real-time monitoring)
+- POST /api/scanner/watch/stop - Stop watch mode
+- GET /api/scanner/watch/status - Get watch mode status
+
 ## OPDS
 
 See [OPDS Feeds](opds/)
 
-## Sync Protocols
+- GET /opds/devices/:deviceId/catalog - Get device catalog
+- GET /opds/devices/:deviceId/search - Search device catalog
+- GET /opds/devices/:deviceId/nav - Get device navigation
+- GET /opds/devices/:deviceId/download/:bookId - Download book
+- GET /opds/devices/:deviceId/cover/:bookId - Get cover image
+- GET /opds/devices/:deviceId/formats/:bookId - List formats
 
-See [KOReader Sync](sync/) and [Kobo Sync](sync/)
+## KOReader Sync Protocol
+
+See [KOReader Sync](koreader/) and [Sync Protocol](sync/koreader-protocol.md)
+
+- POST /api/sync/koreader/progress - Sync reading progress
+- GET /api/sync/koreader/metadata/:uuid - Get book metadata
+- GET /api/sync/koreader/library - Get device library
+- POST /api/sync/koreader/bookmarks - Sync bookmarks
+
+## Kobo Sync Protocol
+
+See [Kobo Sync](kobo/) and [Sync Protocol](sync/kobo-protocol.md)
+
+- POST /api/sync/kobo/markup - Sync markup highlights
+- POST /api/sync/kobo/bookmark - Sync bookmarks
+- POST /api/sync/kobo/v1/analytics/gettests - Analytics endpoint
+- GET /api/sync/kobo/v1/initialization - Initialize Kobo sync
+- POST /api/sync/kobo/sync-from-server - Push content to device
 
 ## WebSocket
 
-See [WebSocket Protocol](websocket/)
+See [WebSocket API](websocket/)
+
+- WS /ws/sync - Real-time sync events and notifications
+
+## Frontend Pages
+
+- GET /login - Login page
+- GET /register - Registration page
+- GET / - Home page
+- GET /bookshelf - Bookshelf page
+- GET /dashboard - User dashboard
+- GET /admin - Admin panel
+- GET /devices-page - Device management page
+- GET /conflicts-page - Conflicts resolution page
+
+## Documentation
+
+- GET /docs - Documentation home
+- GET /docs/* - Show documentation pages
+- GET /docs/api/search - Search API documentation
+- GET /docs/search-index.json - Search index for documentation search
+
+## Health
+
+- GET /health - Health check endpoint