MDEV-15772: Clean up the test

Before killing the server, we must issue FLUSH TABLES in order
to cleanly close any MyISAM system tables, to avoid warnings about
them when restarting.

mysql-test/suite/innodb/r/xa_debug.result

@@ -201,6 +201,7 @@ xa start 'test1';
 insert into t1 values(1);
 xa end 'test1';
 xa prepare 'test1';
+FLUSH TABLES;
 xa recover;
 formatID	gtrid_length	bqual_length	data
 1	5	0	test1

mysql-test/suite/innodb/t/xa_debug.test

@@ -20,6 +20,7 @@ dec $trial;
 
 connection default;
 # Kill and restart the server.
+FLUSH TABLES;
 -- exec echo "wait" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
 -- shutdown_server 0
 -- source include/wait_until_disconnected.inc