Python scripts: reorganise into a separate module

[nikolayilyin]

In order to have a simple configuration for python code in IDEA we need to organize python scripts into a separate module. Because currently there seems to be no simple way in IDEA to configure multi-language module in a project.

The affected python scripts are in the src/main/python folder. There are places in BEAM that call python scripts to do analysis - these places should point to the new paths. If there are any places in documentation with paths to python scripts - these places should be fixed as well.