When I used Ubuntu, there were no such problems. I know also that Windows' file system is case insensitive so maybe it causes the issue.
I also tried to change case sensitivity for git like this:
git config core.ignorecase false
but it didn't help
Some untracked working tree files would be overwritten by checkout. Please move or remove them before you can checkout
And what is the actual file listed as preventing checkout? App.js should not be an untracked one after the rename.
Also just tested with such a rename, and checking out pre-rename state works fine. Does it work at the command prompt for you?
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