Hey there! Thanks for the detailed report and the workflow context.
You’re right, the Agent Window doesn’t currently have an /apply-worktree equivalent. I also realize this creates a catch-22 with the suggestion I made on your other thread, apologies for that.
The team is actively rebuilding worktree support in the Agent Window to bring it closer to the Cursor 2 experience, including native apply and lifecycle management. This is in progress right now.
In the meantime, the agent does create a git branch in the worktree, so you could manually cherry-pick or merge those changes into your main branch via the terminal. Not as seamless as the old Apply button, especially with GitButler in the mix, but it’s the closest interim option.