{
        struct pathspec match_all;
        memset(&match_all, 0, sizeof(match_all));
-       read_tree_recursive(tree, "", 0, 0, &match_all, save_files_dirs, o);
+       read_tree_recursive(the_repository, tree, "", 0, 0,
+                           &match_all, save_files_dirs, o);
 }
 
 static int get_tree_entry_if_blob(const struct object_id *tree,
        read_mmblob(&src2, &b->oid);
 
        merge_status = ll_merge(result_buf, a->path, &orig, base_name,
-                               &src1, name1, &src2, name2, &ll_opts);
+                               &src1, name1, &src2, name2,
+                               &the_index, &ll_opts);
 
        free(base_name);
        free(name1);
        /* get all revisions that merge commit a */
        xsnprintf(merged_revision, sizeof(merged_revision), "^%s",
                  oid_to_hex(&a->object.oid));
-       init_revisions(&revs, NULL);
+       repo_init_revisions(the_repository, &revs, NULL);
        rev_opts.submodule = path;
        /* FIXME: can't handle linked worktrees in submodules yet */
        revs.single_worktree = path != NULL;
        struct diff_queue_struct *ret;
        struct diff_options opts;
 
-       diff_setup(&opts);
+       repo_diff_setup(the_repository, &opts);
        opts.flags.recursive = 1;
        opts.flags.rename_empty = 0;
        opts.detect_rename = merge_detect_rename(o);
 {
        char *temp = xstrdup(path);
        char *end;
-       struct dir_rename_entry *entry = NULL;;
+       struct dir_rename_entry *entry = NULL;
 
        while ((end = strrchr(temp, '/'))) {
                *end = '\0';