Got the same error fatal: index file open failed: Permission denied by run git status, and I checked .git/index by
$ ls -al .git/index
to my surprise, it’s
---------- 1 Kjuly staff 768248 Sep 2 11:07 .git/index
I’ve no idea why & how it changed. Anyway, after I changed it’s permission back to 644 by
$ chmod 644 .git/index
git status works.