Hey, thanks for the report.
Right now, the ManagePullRequest tool in Cloud Agents only supports creating PRs for the workspace root repo. Submodule repos aren’t supported as PR targets. This is a known limitation, discussed here: Cloud Agents + Multiple Repositories (non-monorepo setup) - #3 by Colin.
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.