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/media-items/get_audio_track.md

@@ -40,5 +40,5 @@ answers **403** on every track (same gate as the download endpoint).
 ```bash
 curl -H "Authorization: Bearer $TOKEN" \
   -H "Range: bytes=0-1023" \
-  "http://localhost:8765/api/media-items/550e8400-.../audio/0"
+  "http://localhost:8765/api/media-items/550e8400-.../audio/{track_index}"
 ```