[#5054] make pluginmap generator work again

- Fixed some assumptions that changed along the way with regards to what
  the PhpClassFile class composes and returns. Added the ability to
  aggregate namespaces as well as classes in PhpClassFile, and a getter
  for the namespaces, in order to make the pluginmap_generator work.
- Modified the pluginmap_generator to use the new methods.
Merge pull request #5054