diff: preserve original mode in the index

When updating the index during a diff, preserve the original mode,
which prevents us from dropping the mode to what we have interpreted
as on our system (eg, what the working directory claims it to be,
which may be a lie on some systems.)

src/checkout.c

@@ -211,7 +211,7 @@ static bool checkout_is_workdir_modified(
 	if (baseitem->size && wditem->file_size != baseitem->size)
 		return true;
 
-	if (git_diff__oid_for_entry(&oid, data->diff, wditem, NULL) < 0)
+	if (git_diff__oid_for_entry(&oid, data->diff, wditem, wditem->mode, NULL) < 0)
 		return false;
 
 	/* Allow the checkout if the workdir is not modified *or* if the checkout

src/diff.c

@@ -570,7 +570,7 @@ int git_diff__oid_for_file(
 	git_oid *out,
 	git_diff *diff,
 	const char *path,
-	uint16_t  mode,
+	uint16_t mode,
 	git_off_t size)
 {
 	git_index_entry entry;
@@ -580,13 +580,14 @@ int git_diff__oid_for_file(
 	entry.file_size = size;
 	entry.path = (char *)path;
 
-	return git_diff__oid_for_entry(out, diff, &entry, NULL);
+	return git_diff__oid_for_entry(out, diff, &entry, mode, NULL);
 }
 
 int git_diff__oid_for_entry(
 	git_oid *out,
 	git_diff *diff,
 	const git_index_entry *src,
+	uint16_t mode,
 	const git_oid *update_match)
 {
 	int error = 0;
@@ -600,7 +601,7 @@ int git_diff__oid_for_entry(
 		&full_path, git_repository_workdir(diff->repo), entry.path) < 0)
 		return -1;
 
-	if (!entry.mode) {
+	if (!mode) {
 		struct stat st;
 
 		diff->perf.stat_calls++;
@@ -616,7 +617,7 @@ int git_diff__oid_for_entry(
 	}
 
 	/* calculate OID for file if possible */
-	if (S_ISGITLINK(entry.mode)) {
+	if (S_ISGITLINK(mode)) {
 		git_submodule *sm;
 
 		if (!git_submodule_lookup(&sm, diff->repo, entry.path)) {
@@ -630,7 +631,7 @@ int git_diff__oid_for_entry(
 			 */
 			giterr_clear();
 		}
-	} else if (S_ISLNK(entry.mode)) {
+	} else if (S_ISLNK(mode)) {
 		error = git_odb__hashlink(out, full_path.ptr);
 		diff->perf.oid_calculations++;
 	} else if (!git__is_sizet(entry.file_size)) {
@@ -657,11 +658,14 @@ int git_diff__oid_for_entry(
 	/* update index for entry if requested */
 	if (!error && update_match && git_oid_equal(out, update_match)) {
 		git_index *idx;
+		git_index_entry updated_entry;
 
-		if (!(error = git_repository_index__weakptr(&idx, diff->repo))) {
-			git_oid_cpy(&entry.id, out);
-			error = git_index_add(idx, &entry);
-		}
+		memcpy(&updated_entry, &entry, sizeof(git_index_entry));
+		updated_entry.mode = mode;
+		git_oid_cpy(&updated_entry.id, out);
+
+		if (!(error = git_repository_index__weakptr(&idx, diff->repo)))
+			error = git_index_add(idx, &updated_entry);
  	}
 
 	git_buf_free(&full_path);
@@ -856,7 +860,7 @@ static int maybe_modified(
 			&oitem->id : NULL;
 
 		if ((error = git_diff__oid_for_entry(
-				&noid, diff, nitem, update_check)) < 0)
+				&noid, diff, nitem, nmode, update_check)) < 0)
 			return error;
 
 		/* if oid matches, then mark unmodified (except submodules, where

src/diff.h

@@ -94,7 +94,7 @@ extern int git_diff_delta__format_file_header(
 extern int git_diff__oid_for_file(
 	git_oid *out, git_diff *, const char *, uint16_t, git_off_t);
 extern int git_diff__oid_for_entry(
-	git_oid *out, git_diff *, const git_index_entry *, const git_oid *update);
+	git_oid *out, git_diff *, const git_index_entry *, uint16_t, const git_oid *update);
 
 extern int git_diff__from_iterators(
 	git_diff **diff_ptr,