Custom Subpanel Linked to Custom Module Flex Relate

In my module builder custom module, I have been working through the following two articles:
http://developer.sugarcrm.com/2011/05/16/howto-create-a-flex-relate-for-other-modules/
http://developer.sugarcrm.com/2011/05/18/howto-add-a-subpanel-using-code/
Which work perfectly to add a flex relate field to a custom module for the purpose of relating to other custom modules. I have gotten the subpanel to display when using the custom/extension proposal in the second article, but it gets overwritten when I redeploy the module.
There simply MUST be a way to add a custom subpanel in the same way using either the Builds or Packages directory contents, but for the life of me have been unable to find out. I dont want to add a relationship, but need to have this custom subpanel survive redeployment. Any thoughts please?

Hi,

Have you thought about exporting your custom module from the Module Builder, Making the changes on the exported version and then uploading/installing it through the Module Loader in the Admin Menu? If you really don’t wish to build relationships, this may be another approach to your issue.

Thanks for this John, all well and good except if I am going to modify the package each time I might as well move the subpanel files into place manually anyway. There is a “copy files” function to the manifest.php file but MB overwrites it each time.