I believe one of the selling points of git is that it does not add cruft to each directory as a general rule as it only has one .git directory in the root folde

I believe one of the selling points of git is that it does not add cruft to each directory as a general rule as it only has one .git directory in the root folder. The only time you would need to do that is if you wanted to keep an empty directory in the structure of the git repo. If checking out an empty folder with a dot file in it is not desired you could always add a post checkout hook to delete them. Though in that scheme you would lose your empty dirs on checkin I would wager(not sure though). Edit: you could probably do a precommit hook too to inject the dot files into the empty directories.