Preserve tree filemode in index during checkout

Don't try to determine whether the system supports file modes
when putting the tree data in the index during checkout.  The tree's
mode is canonical and did not come from stat(2) in the first place.

src/checkout.c

@@ -1217,8 +1217,7 @@ static int checkout_update_index(
 
 	memset(&entry, 0, sizeof(entry));
 	entry.path = (char *)file->path; /* cast to prevent warning */
-	git_index_entry__init_from_stat(
-		&entry, st, !(git_index_caps(data->index) & GIT_INDEXCAP_NO_FILEMODE));
+	git_index_entry__init_from_stat(&entry, st, true);
 	git_oid_cpy(&entry.oid, &file->oid);
 
 	return git_index_add(data->index, &entry);

tests/checkout/tree.c

@@ -925,3 +925,26 @@ void test_checkout_tree__fails_when_conflicts_exist_in_index(void)
 
 	git_object_free(obj);
 }
+
+void test_checkout_tree__filemode_preserved_in_index(void)
+{
+	git_oid executable_oid;
+	git_commit *commit;
+	git_checkout_opts opts = GIT_CHECKOUT_OPTS_INIT;
+	git_index *index;
+	const git_index_entry *entry;
+
+	cl_git_pass(git_repository_index(&index, g_repo));
+
+	cl_git_pass(git_oid_fromstr(&executable_oid, "afe4393b2b2a965f06acf2ca9658eaa01e0cd6b6"));
+	cl_git_pass(git_commit_lookup(&commit, g_repo, &executable_oid));
+
+	opts.checkout_strategy = GIT_CHECKOUT_FORCE;
+
+	cl_git_pass(git_checkout_tree(g_repo, (const git_object *)commit, &opts));
+	cl_assert(entry = git_index_get_bypath(index, "executable.txt", 0));
+	cl_assert_equal_i(0100755, entry->mode);
+
+	git_commit_free(commit);
+	git_index_free(index);
+}