ReOrganizes some files, folder, and code

[joaomcteixeira]

This is a large PR but it's mostly concerns file moves and consequent update of the import statements.

• modules in src.haddock where moved to its corresponding place under libs, as discussed.
• the cns related python code was moved to libcns.
• a new cns/ folder now has CNS-related files and does not contains any python. Hence, previous data.toppar/ was moved to cns.toppar. In the future, modular CNS scripts can go here too.
• definitions were moved to core/: exceptions.py, defaults.py, cns_paths.py
• HADDOCK3 paths are now independent from modules (decoupled) and defined lib-wide under __init__
• path definitions pointing to CNS files were improved (see core.cns_paths.py)
• PDBFactory is now libpdb

[joaomcteixeira]

You can better see the result of this PR if you navigate the branch -> https://github.com/joaomcteixeira/haddock3/tree/libpdb/src/haddock