Hey, thanks for the clear report with steps. We can reproduce it on our side. It’s a known bug: the new Agents Window plus worktree loses context and falls back to the base project. I can’t share an ETA for a fix yet, but I logged your report internally.
As a temporary workaround on 3.2.16, open the worktree in a separate Cursor window, not via Open Workspace inside an already open window with the base project. That keeps the contexts separate and Plan mode stays in the worktree. Not perfect, but it should hold until we ship a fix.
If you notice the agent starting to write to the base repo, stop it and check the sidebar, otherwise the changes may land in the wrong place.
We’ll post an update in this thread once there’s news on the fix.