if (envchanged)
                                *envchanged = 1;
                } else if (!strcmp(cmd, "--no-replace-objects")) {
-                       read_replace_refs = 0;
+                       check_replace_refs = 0;
                        setenv(NO_REPLACE_OBJECTS_ENVIRONMENT, "1", 1);
                        if (envchanged)
                                *envchanged = 1;
                } else if (!strcmp(cmd, "--shallow-file")) {
                        (*argv)++;
                        (*argc)--;
-                       set_alternate_shallow_file((*argv)[0]);
+                       set_alternate_shallow_file((*argv)[0], 1);
                        if (envchanged)
                                *envchanged = 1;
                } else if (!strcmp(cmd, "-C")) {