Make `illuminatio run` idempotent

[maxbischoff]

Currently our suggested way of executing illuminatio is illuminatio clean run. As illuminatio run only works the first time, we should either integrate the clean or make the run idempotent by reusing existing resources where sensible. What is your opinion on this?

[hacker-h]

I would also suggest to make clean the default and add something like a keep option for the opposite.

[johscheuer]

I think running clean as the default should work in most cases. Adding a keep flag to not remove all results should be enough.