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/sync/kobo-protocol.md

@@ -6,7 +6,7 @@ Kobo uses a proprietary sync protocol with JSON payloads.
 
 ## Kobo Markup Sync
 
-**Endpoint**: `POST /api/sync/kobo/markup`
+**Endpoint**: `POST /api/sync/kobo/:token/markup`
 **Auth**: Device token required
 **Content-Type**: `application/json`
 
@@ -33,7 +33,7 @@ Kobo uses a proprietary sync protocol with JSON payloads.
 ### Example Request
 
 ```http
-POST /api/sync/kobo/markup
+POST /api/sync/kobo/:token/markup
 Authorization: Bearer device-token
 x-kobo-device: {"DeviceId":"device-id","Model":"Kobo Clara"}
 Content-Type: application/json