This doesn’t always work, because all tool queries and shell commands confirm the files are in the correct positions
The Agent is convinced this new folder is the actual project work folder.
I am able to drag and drop files, but this conflicts with the Apply/Re-Apply/Undo features.
Also sometimes the same file names are created or changed.
Maybe an option is like a controlled merge session/feature, like the Agent Review function, but for the whole batch of results in the branched changes.
I ran three agents to generate a new UI component simultaneously. I’m able to apply code changes generated by GPT 5 Codex High and Composer 1 to the current branch, but the changes created by Claude Sonnet 4.5 failed to apply because of a markdown file the model created and then deleted as shown in the image. I asked the model to delete the git history of this markdown file but it didn’t work.
Steps to Reproduce
Ask the Sonnet 4.5 to create the UI component based on my prompt.
When finished coding, it started creating the markdown file shown in the image but then deleted it as it realized it didn’t follow my Cursor rule that no markdown file should be created for a newly added feature.
After code was generated, hit the Apply All button and the failed to apply worktree to current branch error message popped up.
Expected Behavior
Clicking Apply All will apply changes to the current branch.
I got similar issue described by GitandGeek above using 3x models in parallel. If on one model, it create a file, then via some interaction with me this file is deleted, then I got this error (given below), which is frustating
Failed to apply worktree to current branch: Unable to read file ‘/Users/valentindemange/.cursor/worktrees/dashdoc-1/m3o3V/frontends/apps/web-flow/src/hooks/useSimpleFetch.ts’ (Error: Unable to resolve nonexistent file ‘/Users/valentindemange/.cursor/worktrees/dashdoc-1/m3o3V/frontends/apps/web-flow/src/hooks/useSimpleFetch.ts’)
