Misc cleanup task.

[Carreau]

Those a misc task, that don't deserve an issue in themselves.
They don't need to be done all at once, but can be done in small groups:

• Gen.__init__ takes dummy_progress parameter, it should get it from the config object.
• Gen.collect_package_metadata should likely be folded in __init__, as it is required for many other steps to run.
• Gen.collect_api_docs takes a root parameter, but should likely get this value from self.config