reset: fix mixed reset when using virtual filesystem (again) #651
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This should fix #646, at least in the case that I've been able to verify.
The issue is that reset was setting the skip-worktree bit more frequently than it should have. The previous fix in #494 was focused on the case where a file is added or removed across the diff. However, when the file exists on both sides but still needs to be staged in a mixed reset then we should avoid the skip-worktree bit.
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