clean scripts

We need to review scripts one by one and see if they work or not.
Suggestion how to proceed:
- if they don't work, fix them or move them to scripts/example_notworking.
- if they do, move them to scripts/test for the simplest ones, or to examples/ for complete and well documented scripts

Also, in the end scripts/ should contain only non-simulation script (e.g. rename-class.py, regression-tests.py,...).
Simulations should be only in examples and scripts/test.

Reviewed scripts can be reported here to avoid re-testing them.