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/progress/update_universal_progress.md

@@ -0,0 +1,60 @@
+# Update Universal Progress
+
+Update universal reading progress for a media item.
+
+**Endpoint**: `POST /api/progress/:id`
+**Auth**: Required
+**Content-Type**: `application/json`
+
+## Path Parameters
+
+| Parameter | Type | Required | Description |
+|-----------|------|-----------|-------------|
+| id | string (UUID) | Yes | Media item UUID |
+
+## Request Body
+
+| Field | Type | Required | Description |
+|--------|------|-----------|-------------|
+| percentage | float | No | Progress percentage (0-100) |
+| position | integer | No | Current position in bytes |
+| page | integer | No | Current page number |
+| finished | boolean | No | Whether the book is finished |
+| device_id | string (UUID) | No | Device UUID (optional, for tracking source) |
+
+### Example Request
+
+```json
+{
+  "percentage": 75.5,
+  "position": 1234,
+  "page": 150,
+  "finished": false,
+  "device_id": "device-uuid"
+}
+```
+
+## Response (200 OK)
+
+```json
+{
+  "media_item_id": "uuid",
+  "percentage": 75.5,
+  "position": 1234,
+  "page": 150,
+  "finished": false,
+  "updated_at": "2026-02-08T10:00:00Z"
+}
+```
+
+## Error Responses
+
+| Code | Description |
+|------|-------------|
+| 400 | Invalid request data |
+| 401 | Invalid or expired token |
+| 404 | Media item not found |
+
+## Try It Out
+
+<!-- API Explorer will be inserted here in Phase 3 -->