unpack-trees: fix accidental loss of user changes

For sparse-checkouts, we don't want unpack-trees to error out on files
that are missing from the worktree, so there has traditionally been
logic to make it skip the verify_uptodate() check for these.
Unfortunately, it was skipping the verify_uptodate() check for files
that were expected to *become* SKIP_WORKTREE.  For files that were not
already SKIP_WORKTREE, that can cause us to later delete the file in
apply_sparse_checkout().  Only skip the check for files that were
already SKIP_WORKTREE as well to avoid lightly discarding important
changes users may have made to files.

Note 1: unpack-trees.c is already a bit complex, and the logic around
CE_SKIP_WORKTREE and CE_NEW_SKIP_WORKTREE in that file are no exception.
I also tried just replacing CE_NEW_SKIP_WORKTREE with CE_SKIP_WORKTREE
in the verify_uptodate() check instead of checking for both flags, and
found that it also fixed this bug and passed all the tests.  I also
attempted to devise a few testcases that might trip either variant of my
fix and was unable to find any problems.  It may be that just checking
CE_SKIP_WORKTREE is a better fix, but I'm not sure.  I thought it
was a bit safer to strictly reduce the number of cases where we skip the
up-to-date check rather than just toggling which kind of cases skip it,
and thus went with the current variant of the fix.

Note 2: I also wondered if verify_absent() might have a similar bug, but
despite my attempts to try to devise a testcase that would trigger such
a thing, I couldn't find any problematic testcases.  Thus, this patch
makes no attempt to apply similar changes to verify_absent() and
verify_absent_if_directory().

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

t/t1011-read-tree-sparse-checkout.sh

@@ -197,7 +197,7 @@ test_expect_success 'read-tree will not throw away dirty changes, non-sparse' '
 	grep -q dirty init.t
 '
 
-test_expect_failure 'read-tree will not throw away dirty changes, sparse' '
+test_expect_success 'read-tree will not throw away dirty changes, sparse' '
 	echo "/*" >.git/info/sparse-checkout &&
 	read_tree_u_must_succeed -m -u HEAD &&
 

unpack-trees.c

@@ -2065,7 +2065,9 @@ static int verify_uptodate_1(const struct cache_entry *ce,
 int verify_uptodate(const struct cache_entry *ce,
 		    struct unpack_trees_options *o)
 {
-	if (!o->skip_sparse_checkout && (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
+	if (!o->skip_sparse_checkout &&
+	    (ce->ce_flags & CE_SKIP_WORKTREE) &&
+	    (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
 		return 0;
 	return verify_uptodate_1(ce, o, ERROR_NOT_UPTODATE_FILE);
 }