thodg/libgit2

diff --git a/src/checkout.c b/src/checkout.c
index 539939e..0b6e298 100644
--- a/src/checkout.c
+++ b/src/checkout.c
@@ -1794,9 +1794,6 @@ static int checkout_create_the_new(
 	int error = 0;
 	git_diff_delta *delta;
 	size_t i;
-	int caps = git_index_caps(data->index);
-
-	git_index_set_caps(data->index, caps & ~GIT_INDEXCAP_NO_FILEMODE);
 
 	git_vector_foreach(&data->diff->deltas, i, delta) {
 		if (actions[i] & CHECKOUT_ACTION__DEFER_REMOVE) {
@@ -1818,8 +1815,6 @@ static int checkout_create_the_new(
 		}
 	}
 
-	git_index_set_caps(data->index, caps);
-
 	return 0;
 }
 
@@ -2548,12 +2543,7 @@ int git_checkout_iterator(
 cleanup:
 	if (!error && data.index != NULL &&
 		(data.strategy & CHECKOUT_INDEX_DONT_WRITE_MASK) == 0)
-	{
-		int caps = git_index_caps(data.index);
-		git_index_set_caps(data.index, caps & ~GIT_INDEXCAP_NO_FILEMODE);
 		error = git_index_write(data.index);
-		git_index_set_caps(data.index, caps);
-	}
 
 	git_diff_free(data.diff);
 	git_iterator_free(workdir);
diff --git a/src/index.c b/src/index.c
index dbcc37a..0d2a03e 100644
--- a/src/index.c
+++ b/src/index.c
@@ -987,9 +987,10 @@ static int index_no_dups(void **old, void *new)
  * it, then it will return an error **and also free the entry**.  When
  * it replaces an existing entry, it will update the entry_ptr with the
  * actual entry in the index (and free the passed in one).
+ * trust_mode is whether we trust the mode in entry_ptr.
  */
 static int index_insert(
-	git_index *index, git_index_entry **entry_ptr, int replace)
+	git_index *index, git_index_entry **entry_ptr, int replace, bool trust_mode)
 {
 	int error = 0;
 	size_t path_length, position;
@@ -1021,7 +1022,10 @@ static int index_insert(
 			&position, index, entry->path, 0, GIT_IDXENTRY_STAGE(entry), false)) {
 		existing = index->entries.contents[position];
 		/* update filemode to existing values if stat is not trusted */
-		entry->mode = index_merge_mode(index, existing, entry->mode);
+		if (trust_mode)
+			entry->mode = git_index__create_mode(entry->mode);
+		else
+			entry->mode = index_merge_mode(index, existing, entry->mode);
 	}
 
 	/* look for tree / blob name collisions, removing conflicts if requested */
@@ -1122,7 +1126,7 @@ int git_index_add_frombuffer(
 	git_oid_cpy(&entry->id, &id);
 	entry->file_size = len;
 
-	if ((error = index_insert(index, &entry, 1)) < 0)
+	if ((error = index_insert(index, &entry, 1, true)) < 0)
 		return error;
 
 	/* Adding implies conflict was resolved, move conflict entries to REUC */
@@ -1142,7 +1146,7 @@ int git_index_add_bypath(git_index *index, const char *path)
 	assert(index && path);
 
 	if ((ret = index_entry_init(&entry, index, path)) < 0 ||
-		(ret = index_insert(index, &entry, 1)) < 0)
+		(ret = index_insert(index, &entry, 1, false)) < 0)
 		return ret;
 
 	/* Adding implies conflict was resolved, move conflict entries to REUC */
@@ -1182,7 +1186,7 @@ int git_index_add(git_index *index, const git_index_entry *source_entry)
 	}
 
 	if ((ret = index_entry_dup(&entry, INDEX_OWNER(index), source_entry)) < 0 ||
-		(ret = index_insert(index, &entry, 1)) < 0)
+		(ret = index_insert(index, &entry, 1, true)) < 0)
 		return ret;
 
 	git_tree_cache_invalidate_path(index->tree, entry->path);
@@ -1313,7 +1317,7 @@ int git_index_conflict_add(git_index *index,
 		/* Make sure stage is correct */
 		GIT_IDXENTRY_STAGE_SET(entries[i], i + 1);
 
-		if ((ret = index_insert(index, &entries[i], 1)) < 0)
+		if ((ret = index_insert(index, &entries[i], 1, true)) < 0)
 			goto on_error;
 
 		entries[i] = NULL; /* don't free if later entry fails */
@@ -2537,7 +2541,7 @@ int git_index_add_all(
 		entry->id = blobid;
 
 		/* add working directory item to index */
-		if ((error = index_insert(index, &entry, 1)) < 0)
+		if ((error = index_insert(index, &entry, 1, false)) < 0)
 			break;
 
 		git_tree_cache_invalidate_path(index->tree, wd->path);
diff --git a/tests/index/filemodes.c b/tests/index/filemodes.c
index 58d7935..b390799 100644
--- a/tests/index/filemodes.c
+++ b/tests/index/filemodes.c
@@ -153,6 +153,85 @@ void test_index_filemodes__trusted(void)
 	git_index_free(index);
 }
 
+#define add_entry_and_check_mode(I,FF,X) add_entry_and_check_mode_(I,FF,X,__FILE__,__LINE__)
+
+static void add_entry_and_check_mode_(
+	git_index *index, bool from_file, git_filemode_t mode,
+	const char *file, int line)
+{
+	size_t pos;
+	const git_index_entry* entry;
+	git_index_entry new_entry;
+
+	/* If old_filename exists, we copy that to the new file, and test
+	 * git_index_add(), otherwise create a new entry testing git_index_add_frombuffer
+	 */
+	if (from_file)
+	{
+		clar__assert(!git_index_find(&pos, index, "exec_off"),
+			file, line, "Cannot find original index entry", NULL, 1);
+
+		entry = git_index_get_byindex(index, pos);
+
+		memcpy(&new_entry, entry, sizeof(new_entry));
+	}
+	else
+		memset(&new_entry, 0x0, sizeof(git_index_entry));
+
+	new_entry.path = "filemodes/explicit_test";
+	new_entry.mode = mode;
+
+	if (from_file)
+	{
+		clar__assert(!git_index_add(index, &new_entry),
+			file, line, "Cannot add index entry", NULL, 1);
+	}
+	else
+	{
+		const char *content = "hey there\n";
+		clar__assert(!git_index_add_frombuffer(index, &new_entry, content, strlen(content)),
+			file, line, "Cannot add index entry from buffer", NULL, 1);
+	}
+
+	clar__assert(!git_index_find(&pos, index, "filemodes/explicit_test"),
+		file, line, "Cannot find new index entry", NULL, 1);
+
+	entry = git_index_get_byindex(index, pos);
+
+	clar__assert_equal(file, line, "Expected mode does not match index",
+		1, "%07o", (unsigned int)entry->mode, (unsigned int)mode);
+}
+
+void test_index_filemodes__explicit(void)
+{
+	git_index *index;
+
+	/* These tests should run and work everywhere, as the filemode is
+	 * given explicitly to git_index_add or git_index_add_frombuffer
+	 */
+	cl_repo_set_bool(g_repo, "core.filemode", false);
+
+	cl_git_pass(git_repository_index(&index, g_repo));
+
+	/* Each of these tests keeps overwriting the same file in the index. */
+	/* 1 - add new 0644 entry  */
+	add_entry_and_check_mode(index, true, GIT_FILEMODE_BLOB);
+
+	/* 2 - add 0755 entry over existing 0644 */
+	add_entry_and_check_mode(index, true, GIT_FILEMODE_BLOB_EXECUTABLE);
+
+	/* 3 - add 0644 entry over existing 0755 */
+	add_entry_and_check_mode(index, true, GIT_FILEMODE_BLOB);
+
+	/* 4 - add 0755 buffer entry over existing 0644  */
+	add_entry_and_check_mode(index, false, GIT_FILEMODE_BLOB_EXECUTABLE);
+
+	/* 5 - add 0644 buffer entry over existing 0755 */
+	add_entry_and_check_mode(index, false, GIT_FILEMODE_BLOB);
+
+	git_index_free(index);
+}
+
 void test_index_filemodes__invalid(void)
 {
 	git_index *index;