Most of my projects are either on github or bitbucket, I'm not a fan of adding a whole bunch of other folders to the source code (for example; initializing git in the folder where the server.exe is) so I always initialize my repository in the resources folder.

By initializing a git repo, you always get a .git folder. The server does an attempt on booting up this folder, I think it's safe to say that you can skip every hidden folder/file while booting up resources. It's also not in my list of resources in the server.xml so it shouldn't even try to boot it up in the first place.