[git] How to restore the permissions of files and directories within git if they have been modified?

Try git config core.fileMode false

From the git config man page:

core.fileMode

If false, the executable bit differences between the index and the working copy are ignored; useful on broken filesystems like FAT. See git-update-index(1).

The default is true, except git-clone(1) or git-init(1) will probe and set core.fileMode false if appropriate when the repository is created.

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