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/devices/remove_from_shelf.md

@@ -0,0 +1,43 @@
+# Remove from Shelf
+
+Remove a media item from a device's shelf.
+
+**Endpoint**: `DELETE /api/devices/:id/shelves`
+**Auth**: Required
+**Content-Type**: `application/json`
+
+## Path Parameters
+
+| Parameter | Type | Required | Description |
+|-----------|------|-----------|-------------|
+| id | string (UUID) | Yes | Device UUID |
+
+## Request Body
+
+| Field | Type | Required | Description |
+|--------|------|-----------|-------------|
+| media_item_id | string (UUID) | Yes | Media item UUID to remove from shelf |
+
+### Example Request
+
+```json
+{
+  "media_item_id": "550e8400-e29b-41d4-a716-446655440001"
+}
+```
+
+## Response (204 No Content)
+
+Item removed from shelf successfully.
+
+## Error Responses
+
+| Code | Description |
+|------|-------------|
+| 400 | Invalid request data |
+| 401 | Invalid or expired token |
+| 404 | Device or shelf item not found |
+
+## Try It Out
+
+<!-- API Explorer will be inserted here in Phase 3 -->