[Refactor] We need to re-factor config.py to reflect file folder re-factoring for Incubation

There is file folder paths re-factoring in the scope of INDY-833. It makes valid folder layout for output deb packages and provides required migration.
But it doesn't assume any deep re-factoring of the code base.

We need to perform the following re-factoring on the code level:
1) Separate a number of paths in the config responsible for outputs
2) These paths must be absolute
3) These paths must be configurable for different installations (default, CLI, tests, deb, rpm, Windows, etc.)
4) We need to re-factor the code to not use paths from config only during initialization
5) We need to re-factor the code to use proper paths
6) We need to get rid of BASEDIR (there is no BASEDIR anymore, all paths are absolute).
7) We need to make tests use special config and be consistent.
8) DEB packages should use proper system-dependent configs
9) Required migration must be provided