clearRepoWorkspace was calling updateWorkspace to null out the repo even when there was no local folder, leaving an empty workspace. Now falls through to persistCodebase which correctly removes the entire workspace when both cwd and repoUrl would be null. Co-Authored-By: Paperclip <noreply@paperclip.ing> Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>