Removing non-repository files with git?

I'm writing Autotools code and in the process of development, tons of files are generated.

Is there anyway to tell git to remove all files from a directory that are not part of the repository?

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You can use git-clean. This command will remove untracked files/directories. By default, it will only print what it would have removed, without actually removing them.

Given the -f flag to remove the files, and the -d flag to remove empty directories as well :

git clean -df

Also removing ignored files :

git clean -dfx