Sometimes you get Git messages like
The following untracked working tree files would be overwritten by checkout
The following command can be helpful in that case.
git clean -d -fx ""
-x means ignored files are also removed as well as files unknown to git.
-d means remove untracked directories in addition to untracked files.
-f is required to force it to run.
I've learned this by a discussion on Stackoverflow: http://goo.gl/I9NMxO.