Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again.  imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy?