Yarn upgrade breaks entire repo with "EACCES: permission denied, rmdir"

[BlueRaja]

Bug description

Running yarn upgrade with any dependency in our repo gives me

error An unexpected error occurred: "EACCES: permission denied, rmdir '/Users/myUserName/git/myRepoName/node_modules/@ember-data/private-build-infra/node_modules/.cache/esm'"

After this, I'm unable to run our app or yarn install ever again. Running yarn install gives the same error as above, and running the app gives dependency errors.

What is the current behavior?
See above

What is the expected behavior?
See above

Steps to Reproduce
See above. It repros 100% of the time in our repo. Our repo has multiple package-directories, each with its own node_modules folder. After running yarn upgrade, none of them work.

I am just running yarn as usual, not with sudo

Workarounds
I tried the following, none of which work:

• chmod and chown on all node_modules folders
• Deleting all node_modules folders
• Revert package.json and yarn.lock (using git)
• chmod and chown on ~/Library/Caches/Yarn, /usr/local/share/Library/Caches/Yarn, ~/.yarn, ~/.config/yarn/
• Deleting all of the above folders (careful with the last one, it will delete your global installs)
• yarn cache clean
• yarn lerna clean
• yarn install --check-files
• yarn install --force
• Uninstalling yarn completely and reinstalling

The only thing that works is:

• Delete THE ENTIRE REPO and check it out again from git.

Environment

• Node Version: 10.20.1
• Yarn v1 Version: 1.22.4
• OS and version: OSX 10.13.6