In our repository some files and folders are ignored. Of interest here are:
First, you can add an ignored file to the index and commit it.
You just need to to git add --force -- /path/to/file
.
Second, you can add the setup files themselves: they contain private data.
You may consider the template approach, based on a content filter driver which, on checkout, would generate those files (as private non-versioned files) based on:
See for instance "How to keep different content of one file in my local and github repository?"
This is a bit hackish, but how about symlinking them from a separate repo into your main project?