Just a note: the theme subtemplate currently adds a registration of the theme to the configure.zcml of the addon package.
We will change this, because the resulting zcml file comes from lxml then and has a different formating.
We decided to just print a note, what the developer has to do.
This will probably apply to other updating files task later as well.
But it's the best way to not mangle the files.
Be aware that the subtemplates will override files, if they already exist.
So always use a clean repository before using them!