Create new helpers in regression tests

* Avoid future duplication of code
* Run tests in a unique directory to clean stuff more easily
Add python bytecode files (*.pyc) in gitignore
Put testing procedure out of the test class

The test class now contains only the very high level of test. All the
implementation details are in helper functions.
Test the --flat option of PBassign
Ignore test outputs from the repository
Add regression tests for option phipsi of PBassign