fix(docs): Work Order 2 — correct stale paths (11 docs + 3 Bruno)

Fix all wrong-path artifacts identified by the audit:
- Kobo sync endpoints (init/bookmark/markup/sync-from-server/analytics): add
  missing :token device segment (6 doc files incl. kobo-protocol.md)
- Highlights/notes update+delete: add missing /:id media-item prefix
- media-items/download_media_item.md: removed (static /uploads route, not an
  API endpoint; info about the file route is recoverable from OPDS docs)
- Bruno: /libraries/visible -> /visibility, /collections/books missing id,
  /audio/0 -> track_index
- operations/troubleshooting.md: same /libraries/visible -> /visibility fix
- media-items/get_audio_track.md + get_audio_chapters.md: /audio/0 examples fixed
- Deleted monolithic docs/developer/api-reference.md (duplicate of split docs)
- Fixed 4 stale entries in docs/developer/api/api-reference.md (split index)

Audit re-run: orphan docs 0, orphan Bruno 6 (all scenario files with literal IDs).

docs/developer/api/api-reference.md

@@ -256,11 +256,11 @@ See [KOReader Sync](koreader/) and [Sync Protocol](sync/koreader-protocol.md)
 
 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
+- POST /api/sync/kobo/:token/markup - Sync markup highlights
+- POST /api/sync/kobo/:token/bookmark - Sync bookmarks
+- POST /api/sync/kobo/:token/v1/analytics/gettests - Analytics endpoint
+- GET /api/sync/kobo/:token/v1/initialization - Initialize Kobo sync
+- POST /api/sync/kobo/:token/sync-from-server - Push content to device
 
 ## WebSocket