git remove file from repository but leave it on file system

Just:

git rm --cached file [file ...]

Of course you'll need to make sure the offending files are added to your .gitignore so they don't get recommitted straight away

If you want to keep the file in the repository, you can use:
git update-index --assume-unchanged <fileName>

This keeps the current version of the file in the index, but you can change it all you want and git will ignore those changes.