Hey @prasad_subrahmanya!
I can confirm that multi-repo support for Cloud Agents isn’t available today. It’s top of mind (it would be immensely helpful to us here at Cursor as well).
Submodules aren’t a great workaround here. Cloud Agents explicitly skip fetching submodule contents during setup (--recurse-submodules=no), and even if you (or the agent) manually initialized them, you wouldn’t be able to edit or make PRs to those repos.