git clean - Cleaning the Git repository to be able to merge with remote

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 ""

See http://www.kernel.org/pub/software/scm/git/docs/git-clean.html

-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.