Fix bp2build-progress.

Always setting set() in module adjacency list was overwriting
dependencies. Now we default it to set such that it will only add when
not existing.

For json-only:
* we were only analyzing a single variant, which lead to missing a
  number of dependencies.
* Variants changed from a map to an array of maps

Test: run bp2build-progress.py
Change-Id: I1c321ecbc6d99f99125976144dc3a9d0bc0ba78d