Hi I saw your latest message in the !gnusocial group but I lost it and I can't answer directly, I have some troubles with the federation.
Yes I'm working on a new theme and the install layout but I think the following... With the current system, themes only allow designers to overwritte some css styles but we need more, we need to edit the document object adding classes and more elements. To achieve this we need to overwritte the lib folder from the active theme, in some point the gnusocial core must see if a a file exists in the active theme and use it instead the original one.
Modern cms like joomla o wordpress use that technique for modify core scripts.
What do you think about that?