Git, files marked for deleting and won't commit

I'm using PHPStorm to manage my projects, one of which is under Git control.

I had a number of files which I renamed and changed the capilisation.

The problem I have now is that PHPStorm shows the files are marked for deletion (gray), I can commit the project ok, but files marked for deleting don't get commited or pushed to github.

I'm struggling to figure out what I can do. The files are NOT to be deleted, I need them in the project.
SheppardDigitalAsked:
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SheppardDigitalAuthor Commented:
I've managed to fix this.

I ran 'git status' which showed that the files were due to be deleted/commited in a folder called 'repository', where as I has renamed the folder to 'Repository'.

I renamed the folder, and everything seems to be working as it should be again.

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SheppardDigitalAuthor Commented:
Resolved myself
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