Stubgen improvements: preserving existing annotations (#3169)

This PR modifies heavily the stubgen to be able to create better stubs
when processing already annotated files (Implements #2106 ).
It essentially adds annotations on the stubs for:

* Variables/attributes with annotations
* Annotations on functions/methods
* TypeVar declarations
* Type Aliases

It also adds some fixes (handling of generics as base classes,
some formatting fixes in the output) that were natural consequences
of some of the refactoring I made.