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Troubleshoot Agent Manager and Worktrees

Agent Manager depends on a valid Git repository and performs work in directories separate from the main checkout.

A worktree cannot be created​

Confirm that the open folder is a Git repository, the selected base branch exists, and the requested branch is not already checked out in another worktree. Review the Reasoning output channel for the Git error.

Setup fails​

Open the worktree terminal and review the setup output. Check project prerequisites, package access, environment templates, and whether the .aicockpit setup script is safe to run more than once.

Fix the script or the missing prerequisite so future worktrees set up correctly, then run the missing steps in this worktree's terminal. Do not delete a worktree solely because setup failed. Run script starts the project's run script; it does not run setup again.

Changes appear in the wrong place​

Confirm the selected worktree and the terminal's working directory. Files changed in the main checkout do not belong to a managed worktree's diff.

Pull request status is unavailable​

Local changes do not require a pull request. Pull request status uses the GitHub CLI: install it and run gh auth login. Agent Manager shows GitHub CLI not installed or GitHub authentication required when one of them is missing. Also confirm that the branch has a pull request on GitHub.