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/kobo/markup_sync.md

@@ -0,0 +1,71 @@
+# Markup Sync
+
+Sync markup highlights and annotations from Kobo device.
+
+**Endpoint**: `POST /api/sync/kobo/markup`
+**Auth**: Required (Device authentication)
+
+## Device Authentication
+
+This endpoint requires device authentication (not user JWT). Kobo devices authenticate using their device credentials and access tokens.
+
+## Request Body
+
+| Field | Type | Required | Description |
+|--------|------|-----------|-------------|
+| bookmarks | array | Yes | Array of bookmark/markup objects |
+
+### Bookmark Object
+
+| Field | Type | Required | Description |
+|--------|------|-----------|-------------|
+| BookmarkID | string | Yes | Unique bookmark ID |
+| ContentID | string | Yes | Book content ID |
+| StartPosition | integer | Yes | Highlight start position |
+| EndPosition | integer | No | Highlight end position |
+| Text | string | No | Highlighted text |
+| Annotation | string | No | User annotation |
+| DateCreated | string | Yes | ISO 8601 timestamp |
+| Chapter | string | No | Chapter title |
+| Hidden | boolean | No | Whether bookmark is hidden |
+
+### Example Request
+
+```json
+{
+  "bookmarks": [
+    {
+      "BookmarkID": "bookmark123",
+      "ContentID": "book-uuid",
+      "StartPosition": 1234,
+      "EndPosition": 1456,
+      "Text": "Highlighted text from book",
+      "Annotation": "My annotation",
+      "DateCreated": "2026-02-08T10:00:00Z",
+      "Chapter": "Chapter 1",
+      "Hidden": false
+    }
+  ]
+}
+```
+
+## Response (200 OK)
+
+```json
+{
+  "message": "Markup synced successfully",
+  "synced_count": 1
+}
+```
+
+## Error Responses
+
+| Code | Description |
+|------|-------------|
+| 401 | Device authentication failed |
+| 400 | Invalid request data |
+| 404 | Device or book not found |
+
+## Try It Out
+
+<!-- API Explorer will be inserted here in Phase 3 -->