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/kobo/initialization.md

@@ -4,7 +4,7 @@
 
 Initialize Kobo device sync.
 
-**Endpoint**: `GET /api/sync/kobo/v1/initialization`
+**Endpoint**: `GET /api/sync/kobo/:token/v1/initialization`
 **Auth**: Required (Device authentication)
 
 ## Device Authentication
@@ -22,7 +22,7 @@ This endpoint requires device authentication (not user JWT). Kobo devices authen
 ### Example Request
 
 ```http
-GET /api/sync/kobo/v1/initialization
+GET /api/sync/kobo/:token/v1/initialization
 X-Device-ID: 550e8400-e29b-41d4-a716-446655440000
 X-Device-Key: device-auth-key
 ```