Linearize the tree of modules and submodules when the modules
are set on the manifest, while filtering out disabled modules
at the same time.
Skip source-less modules when building; this makes it possible
to have modules that only contain submodules.
With this approach, we use the tree structure of modules for
serializing and deserializing to and from json, while using
a linear list of modules for building.
Matthias Clasen
e25e379a2a