This is some what a known limitation. Currently there is no workaround as such which could deal with this issue.
What I did was to set up another VPP for those files. I simply pointed the IconBase to "MyDir/myfile" and created a VPP for App_Themes/.../editor/MyDir or whatever the path will be. This way you can put the files wherever you want, but of course it will need an entry in web.config so it's not self-contained in that way.
BTW, if you figure out how to make a VPP physicalpath relative to the application root (so you don't have to specify the full physical path) I'm interested :)
An other way is to use the mapped provider, but that will require a web.config entry for every file, since the mapped provider currently can't be configured to map a directory.
Magnus I did see your forum post with the VPP solution and it's serainly a good workaround. Thank you for the sugestion!
Hopefully EPiServer changes it so that a GUI plugin can be selfcontained.
With CMS5 and VPPs the IconBase dicectory is now pointing towards the AppTheme under program files\EPiServer......;
Is it possible to override this for a GUI-plugin? I want to make the plugin "selfcontained" and have all files within one folder structure and not have to shotgun deploy all over the filesystem ;-)