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    Note that you might actually not have a dirty working directory: there's a bug in git prior to 1.7.7.1 which means git doesn't refresh its internal indexes when running filter-branch. So try running these two commands anyway - unless anyone knows of a less hacky way to force index refresh. (More discussion of this on this question .) Commented May 16, 2012 at 11:04
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    From a comment added at the link above: git update-index -q --ignore-submodules --refresh should update the index! Commented May 16, 2012 at 15:17
  • You can use git stash pop to apply the last stashed changes and remove them from the stash list. apply will apply the changes but a git stash list still shows the stashed changes. Commented Mar 30, 2017 at 17:11