Why do some files stay Modified / Blue on Commit?

I'm working remotely with a GitHub repository, but when I commit a subset of my files are staying Blue / Modified instead of going back to Black / Unmodified.  This is making it tedious to make further commits, as I need to manually specify the files to commit instead of committing whole directory and letting PyCharm only commit the necessary files.

What am I missing?

  • Brett
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What is git status (on the command line) saying in one of the directories that has modified files after a commit?
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For other with the same issue - 

I had the same issue with an existing repo that I added to github. I opened a command prompt and did "git status" . It showed the same files as both untracked ( not added ) and modified . I did a git add .  follow by a git commit -m .. which fixed it. 

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