Hey, thanks for the detailed report. This is a known issue. Agent Grep and Glob build their search off the git tree, and nested git repos that aren’t registered as submodules with no entry in .gitmodules end up invisible to these tools. That’s why Read, terminal rg, and Ctrl+Shift+F work since they scan the filesystem directly, but Grep and Glob don’t.
I’ve passed this to the team. For now, a workable workaround is to add a rule in .cursor/rules so the agent uses the terminal for search:
When searching for files in this project, prefer using terminal commands (find, grep, rg)
instead of the built-in glob/grep tools, as this workspace contains nested git repositories
which the glob/grep tools currently don't handle correctly.
Not ideal, but it unblocks you. Let me know if you need anything else.