checkout: ignore skip-worktree when virtual

[derrickstolee]

As documented in microsoft/vfsforgit#1812, attempting to restore a file fails when using either of these commands in a VFS for Git repo:

  git restore --source=<commit> <path>
  git checkout <commit> -- <path>

To discover the issue, I debugged such a call and found that since opt->ignore_skipworktree is not set, that the restore will not update the index when the file is not hydrated.

I verified that this works as expected, including that the file on-disk is projecting the new index version.

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• [X] This change only applies to the virtualization hook and VFS for Git.