Why do excluded files keep reappearing in my git sparse checkout?

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The skip-worktree bit can be modified with git update-index --skip-worktree. When you notice the files present you can check git ls-files -v |grep ^S (S being a file marked with skip-worktree).

But as the #git folks say, if you see odd behavior it is most likely a bug in git. After all, this is quite esoteric feature. You should probably report your findings to the git mailing list.

Edit: Also, if you are using git 1.7.7.6, I strongly recommend upgrading. 1.7.10 tree is way ahead, and I think there is a strong chance it will fix your problems.

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