The test case probably describes the test scenario the best. We have a
patch to modify some file but the base file is gone. Because
check_preimage() finds an index entry with the same old_name, it tries
to restore the on-disk base file with cached content with
checkout_target() and move on.

If this old_name is i-t-a, before this patch "apply -3" will call
checkout_target() which will write an empty file (i-t-a entries always
have "empty blob" SHA-1), then it'll fail at verify_index_match()
(i-t-a entries are always "modified") and the operation is aborted.

This empty file should not be created. Compare to the case where
old_name does not exist in index, "apply -3" fails with a different
error message "...: does not exist" but it does not touch
worktree. This patch makes sure the same happens to i-t-a entries.

load_current() shares the same code pattern (look up an index entry,
if on-disk version is not found, restore using the cached
version). Fix it too (even though it's not exercised in any test case)

Signed-off-by: Nguyễn Thái Ngọc Duy <pclo...@gmail.com>
---
 builtin/apply.c       |  4 ++--
 t/t2203-add-intent.sh | 16 ++++++++++++++++
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/builtin/apply.c b/builtin/apply.c
index 76b58a1..b185c97 100644
--- a/builtin/apply.c
+++ b/builtin/apply.c
@@ -3348,7 +3348,7 @@ static int load_current(struct image *image, struct patch 
*patch)
                die("BUG: patch to %s is not a creation", patch->old_name);
 
        pos = cache_name_pos(name, strlen(name));
-       if (pos < 0)
+       if (pos < 0 || ce_intent_to_add(active_cache[pos]))
                return error(_("%s: does not exist in index"), name);
        ce = active_cache[pos];
        if (lstat(name, &st)) {
@@ -3501,7 +3501,7 @@ static int check_preimage(struct patch *patch, struct 
cache_entry **ce, struct s
 
        if (check_index && !previous) {
                int pos = cache_name_pos(old_name, strlen(old_name));
-               if (pos < 0) {
+               if (pos < 0 || ce_intent_to_add(active_cache[pos])) {
                        if (patch->is_new < 0)
                                goto is_new;
                        return error(_("%s: does not exist in index"), 
old_name);
diff --git a/t/t2203-add-intent.sh b/t/t2203-add-intent.sh
index bb5ef2b..96c8755 100755
--- a/t/t2203-add-intent.sh
+++ b/t/t2203-add-intent.sh
@@ -95,5 +95,21 @@ test_expect_success 'apply adds new file on i-t-a entry' '
        )
 '
 
+test_expect_success 'apply:check_preimage() not creating empty file' '
+       git init check-preimage &&
+       (
+               cd check-preimage &&
+               echo oldcontent >newfile &&
+               git add newfile &&
+               echo newcontent >newfile &&
+               git diff >patch &&
+               rm .git/index &&
+               git add -N newfile &&
+               rm newfile &&
+               test_must_fail git apply -3 patch &&
+               ! test -f newfile
+       )
+'
+
 test_done
 
-- 
2.3.0.rc1.137.g477eb31

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