You need to clone the repository if you have not done this already, delete the folders and commit+push the change.
This will delete the file moving forward. There is of course no good way to delete the file's existence in previous commits.
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The folder can be deleted from the history with filter-branch http://git-scm.com/docs/git-filter-branch , but I think that is not necessary here (unless it contains a large amount of binary data).
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