Bug #29198 mysqlmanager problems with replication

Description:
I setup mysqlmanager to manage mysql，i stop a instance and then change some of the replication,such as server-id/slave_net_timeout and so on,then start the instance,but these options don't take affected.

How to repeat:
terminal 1:
(root:localhost:)(none)> show global variables like 'slave_net_timeout';
+-------------------+-------+
| Variable_name     | Value |
+-------------------+-------+
| slave_net_timeout | 3600  |
+-------------------+-------+

(root:localhost:)(none)> show global variables like 'server_id';
+---------------+--------+
| Variable_name | Value  |
+---------------+--------+
| server_id     | 1      |
+---------------+--------+

terminal 2:
(yejr:localhost:)(none)> stop instance mysqld1;
Query OK, 0 rows affected (1.20 sec)

(yejr:localhost:)(none)> set mysqld1.slave_net_timeout=10;
Query OK, 0 rows affected (0.00 sec)

(yejr:localhost:)(none)> set mysqld1.server-id=1;
Query OK, 0 rows affected (0.00 sec)

(yejr:localhost:)(none)> start instance mysqld13306;
Query OK, 0 rows affected (0.00 sec)
Instance started

cat my.cnf
[mysqld1]
......
replicate-same-server-id=0
slave_net_timeout=10
......

back to terminal 1:
(root:localhost:)(none)> show global variables like 'slave_net_timeout';
+-------------------+-------+
| Variable_name     | Value |
+-------------------+-------+
| slave_net_timeout | 3600  |
+-------------------+-------+

(root:localhost:)(none)> show global variables like 'server_id';
+---------------+--------+
| Variable_name | Value  |
+---------------+--------+
| server_id     | 1      |
+---------------+--------+

there is no difference with the first result.

Thank you for the report.

Verified as described. All options are not getting updated.

Workaround: restart mysqlmanager.

The instance manager is deprecated in 5.1 and discontinued in 6.0