refactor: only one command with options --extract, --cluster, --plot etc

[jniediek]

Use only one command 'combinato' with options such as --cluster --plot-extracted --combine etc.
This would clean up the directory and make handling of options easier for the user.
Also, it could incorporate a logger that writes out options etc easily.
Also, this would allow to add an option --all-work that just runs the whole processing chain

but it's too much work now