Hey, thanks for the report. You’re right that there’s a difference between the two features.
The custom prompts in .cursor/BUGBOT.md are currently used only by Bugbot’s PR review integration on GitHub/GitLab, as documented here: Bugbot | Cursor Docs
The “Find Issues” feature in Cursor IDE is a separate implementation that doesn’t currently consider these custom prompt files.
This seems like a functionality gap. I’ll pass this on to the team.
There’s already a related feature request here: Rules for Review agent
In the meantime, the GitHub/GitLab integration method should work with your custom prompts as expected.