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).

bruno/collections/Get Book Collections.yml

@@ -5,7 +5,7 @@ info:
 
 http:
   method: GET
-  url: "{{base_url}}/api/collections/books"
+  url: "{{base_url}}/api/collections/{{collection_id}}/books"
   body:
     type: json
     data: |-
@@ -27,7 +27,7 @@ docs: |-
   
     **Method:** GET
   
-    **Endpoint:** /api/collections/books
+    **Endpoint:** /api/collections/{{collection_id}}/books
   
     **Authentication:** Required (Bearer token)