Just add on the --prune-empty option: git filter-branch --tree-filter 'rm -r -f my_folder' --prune-empty -f HEAD (And of course, if you have other refs, you might want to rewrite everything with -- --all instead of just HEAD. ) Note that this isn't compatible with --commit-filter; in that case, Charles Bailey has your answer.
Just looking a the documentation for filter-branch, you should be able to do this: git filter-branch --commit-filter 'git_commit_non_empty_tree "$@"' HEAD.
This works too if I use the -f flag – Paul Pladijs Mar 21 '11 at 15:00 +1 for this. Very useful if you have converted an svn repository, which normally generates a lot of empty commits – Fabio Jun 20 '11 at 22:06.
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