I've noticed that if I copy the barceloneta theme then the manifest.cfg is dynamically updated. For example if I copy barceloneta and create a theme called 'gizzada' in the manifest.cfg the rules, prefix, development.css etc.. all end up being in the gizzad namespace.
Okay... I made a filesystem theme that mimics barceloneta as best as possible (ships with it's own less files etc..) and the copying behaviour now works.
When I tried to have my theme inherit from barceloneta rather than have it's own less files that did not work.