unpack-trees: do not mark a dirty path with SKIP_WORKTREE

If a path is dirty, removing from the working tree risks losing data.
As such, we want to make sure any such path is not marked with
SKIP_WORKTREE.  While the current callers of this code detect this case
and re-populate with a previous set of sparsity patterns, we want to
allow some paths to be marked with SKIP_WORKTREE while others are left
unmarked without it being considered an error.  The reason this
shouldn't be considered an error is that SKIP_WORKTREE has always been
an advisory-only setting; merge and rebase for example were free to
materialize paths and clear the SKIP_WORKTREE bit in order to accomplish
their work even though they kept the SKIP_WORKTREE bit set for other
paths.  Leaving dirty working files in the working tree is thus a
natural extension of what we have already been doing.

Reviewed-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

unpack-trees.c

@@ -500,8 +500,11 @@ static int apply_sparse_checkout(struct index_state *istate,
 		 * also stat info may have lost after merged_entry() so calling
 		 * verify_uptodate() again may fail
 		 */
-		if (!(ce->ce_flags & CE_UPDATE) && verify_uptodate_sparse(ce, o))
+		if (!(ce->ce_flags & CE_UPDATE) &&
+		    verify_uptodate_sparse(ce, o)) {
+			ce->ce_flags &= ~CE_SKIP_WORKTREE;
 			return -1;
+		}
 		ce->ce_flags |= CE_WT_REMOVE;
 		ce->ce_flags &= ~CE_UPDATE;
 	}