Thank you for looking into this issue, and helping resolve this!
I just attempted to re-index some doc sources, and it looks like the indexing is working now.
Log here:
2024-12-16 01:55:11.168 [info] Creating Indexing Repo client: https://repo42.cursor.sh
2024-12-16 01:55:11.337 [info] InternalRepoInfo constructor with preferredEmbeddingModel 0
2024-12-16 01:55:11.347 [info] Creating merkle client.
2024-12-16 01:55:11.347 [info] Done creating merkle client.
2024-12-16 01:55:11.347 [info] Doing a startup handshake.
2024-12-16 01:55:11.362 [info] Finished initializing merkle tree in 4.890480000000025 ms.
2024-12-16 01:55:11.363 [info] Doing the initial handshake with hash: 1a0d9f57918cb7b3c26bf89ba78555f0a04e4450ebab899e6efe8efbfb3438cc
2024-12-16 01:55:11.366 [info] Handshake start
2024-12-16 01:55:11.710 [info] Handshake timing: 347.172544
2024-12-16 01:55:11.711 [info] Handshake result: {"status":"STATUS_UP_TO_DATE","repoName":"b4203cac-67ca-4257-a907-12a6cd3c4727"}
2024-12-16 01:55:11.711 [info] Starting fast remote sync.
2024-12-16 01:55:11.711 [info] Total num embeddable files: 1
2024-12-16 01:55:11.716 [info] Root hash: 1a0d9f57918cb7b3c26bf89ba78555f0a04e4450ebab899e6efe8efbfb3438cc
2024-12-16 01:55:11.716 [info] Finished indexing repository.
2024-12-16 01:55:11.716 [info] Indexing job successfully done or aborted.
2024-12-16 01:55:12.968 [info] Creating Indexing Repo client: https://repo42.cursor.sh
2024-12-16 01:55:12.970 [info] InternalRepoInfo constructor with preferredEmbeddingModel 0
2024-12-16 01:55:12.973 [info] Creating merkle client.
2024-12-16 01:55:12.973 [info] Done creating merkle client.
2024-12-16 01:55:12.973 [info] Doing a startup handshake.
2024-12-16 01:55:12.980 [info] Finished initializing merkle tree in 0.6869209999999839 ms.
2024-12-16 01:55:12.981 [info] Doing the initial handshake with hash: 1a0d9f57918cb7b3c26bf89ba78555f0a04e4450ebab899e6efe8efbfb3438cc
2024-12-16 01:55:12.983 [info] Handshake start
2024-12-16 01:55:13.251 [info] Handshake timing: 270.34418300000016
2024-12-16 01:55:13.252 [info] Handshake result: {"status":"STATUS_UP_TO_DATE","repoName":"b4203cac-67ca-4257-a907-12a6cd3c4727"}
2024-12-16 01:55:13.252 [info] Starting fast remote sync.
2024-12-16 01:55:13.252 [info] Total num embeddable files: 1
2024-12-16 01:55:13.252 [info] Root hash: 1a0d9f57918cb7b3c26bf89ba78555f0a04e4450ebab899e6efe8efbfb3438cc
2024-12-16 01:55:13.252 [info] Finished indexing repository.
2024-12-16 01:55:13.252 [info] Indexing job successfully done or aborted.
Some sources that were failing before have completed indexing now, and some other sources are still indexing (for me), but this seems to be working now!
Thank you for your help restoring this functionality @ericzakariasson !!