I did a plan mode across 3 agents, claude-4.5-sonnet, gpt-5-codex, composer-1, and after claude generated 4274 new lines of code, and I clicked “Apply All” Cursor informed me that it couldn’t find the files.
Fortunately, I worked around it by asking it to manually copy and it is doing that now, but this is a pretty serious error! Hopefully one that can be easily fixed.
For others: the prompt that worked for me was:
I am trying to apply these changes, but Cursor says it can’t find the files. Can you copy them onto the main? (not the worktree)
Steps to Reproduce
create a plan mode with 3 agents.
do not set up the bash script for worktrees (note: The Learn More link did not take me to any documentation about worktrees)
click “Apply All” after building the plan
Operating System
MacOS
Current Cursor Version (Menu → About Cursor → Copy)
Hey, thanks for the report. It looks like a bug in the new worktree‑based multi‑agent system in v2.0.34. Several other users are seeing similar issues where “Apply All” can’t find files generated in worktrees.
Great workaround, your manual copy is the best temporary fix right now.
I’ll pass this to the team. Could you also share:
The exact error message Cursor showed when clicking “Apply All”
Whether you can see the generated files in ~/.cursor/worktrees/
Also, could you update to the latest version and let me know if the issue still persists?
Hi, I finally had a chance to try multiple agents again, and with the latest cursor I am still getting the exact same error
Failed to apply worktree to current branch: Unable to read file '/Users/gregory.beaver/.cursor/worktrees/platform/rsqsV/dashboard/app/javascript/src/lib/validation/errorKeys.ts' (Error: Unable to resolve nonexistent file '/Users/gregory.beaver/.cursor/worktrees/platform/rsqsV/dashboard/app/javascript/src/lib/validation/errorKeys.ts')
The issue is that it is trying to copy files I had already asked it to reject. I iterated after the initial build. It appears to be using the initial files instead of the final ones