staged files not really being staged

I am in a weird twilight-zone of a git problem in xcode. I specify some files to be staged and it fails to do with no warning of any sort. So I cannot commit them or apply stashed changes to them. I can do it one.file.at.a.time.

I have over 11k intermediate files that .gitignore won't ignore, nor stage nor commit to do anything so I could stop tracking them.

staged files not really being staged
 
 
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