I raised this question also, because at the moment we're having different directories for modules and extensions ... and there're also themes which could be distributed with the package manager.
I think composer uses just one (1) directory to store the files. In its case it's 'vendor', but this can be customized, so for Yii this would be 'extensions'.
At the moment we could put all modules under extensions, we'd simply have to configure the modules with a class property. I think this would be also possible for themes, if you change the basePath property - the only thing which would not work then is using the baseUrl property, because it would be inside the protected/extensions folder.
I am working on this feature for Phundament 3, but it's not ready yet. If you want to you can have a look at these two composer.json files to get an impression:
1. phundament (skeleton) --> download p3media
2. p3media --> download p3extensions
PS: Just found some slides from Nils (composer developer) http://www.slideshar...group-karlsruhe