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git: is_tracked: use ls_files instead of walking the index (iterative…
…#3677) Current implementation doesn't work with directories, which results in hard-to-debug bugs like iterative#3561. The bug that made us walk through index manually is now fixed in gitpython, so we can simply use `ls_files` from now on. Added some tests to prevent this from happening in the future. Fixes iterative#3561
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