Reorganize purldb repo

We have a lot of related code in different places. For example, the `minecode/visitor` and `minecode/mapper` modules have code that is logically together, but is currently separated. Reorganizing the repo helps with clarity and focuses the specific workflow we want.

We should organize code to reflect the multi-level data collection we want to do:

1. Collect name, version, checksum
2. Collect metadata from registry
3. Collect package and scan

See also:
- https://github.com/nexB/purldb/issues/521
- https://github.com/nexB/purldb/issues/283