Today all of our workflows started failing because we trigger cloud agents in a repo that has submodules. The agents are prompted to open PRs in any number of the submodules as one of the steps. The submodule PRs fail with some message like “the built-in PR tool only targeted the workspace root repo“.
As far as I can tell this seems like a behavior change with the github integration in cursor, not a config issue on our end.
Steps to Reproduce
run a cloud agent for a repo that has a submodule
prompt the agent to create a PR for the submodule repo
Expected Behavior
The PR is opened for the submodule
Operating System
Linux
Version Information
This is in a cloud agent.
For AI issues: which model did you use?
GPT-5.4 High
For AI issues: add Request ID with privacy disabled
If this used to work for you, the agent was probably using a workaround like the gh CLI to create PRs in submodule repos, and a recent change in how agents handle PR operations may have affected that behavior. Can you confirm if agents previously used the gh CLI or something similar to open PRs in submodule repos?
Multi-repo support for Cloud Agents isn’t available yet. I’ve shared this with the team, and your automation plus submodules case is a good reason to prioritize it.
As a possible workaround, you can try explicitly telling the agent in your prompt to use gh pr create for PRs in submodules instead of the built-in PR tool. No guarantee it’ll work reliably, but it’s worth a try.
Let me know if that helps, or if you have any extra details on how it worked before.
After more investigation, we had a gh cli configured that had broken when a team member rebuilt the team environment incorrectly. This issue is resolved