Stage and pipeline related documentation touch ups

[thehrh]

A few small things that I encountered while trying to get up to speed with core functionality:

• pipeline.py main script docstring adapted (broken, needs to be fixed or removed)
• stage base class: docstring updated
  • no cake vs. pi distinction anymore, right? ("pisa pi" still mentioned in a few other places, but meaning not necessarily clear to a newcomer)
  • lacking effect of promised effect of debug_mode as far as I can tell
  • missing parameters error_method and profile, and other superficial things
  • also cleaned up some left-over references to removed objects in comments
• updated table of directory contents in stages/README.MD (and added expected_params to list of std_kwargs)
• given the importance of the concept, expanded introductory text on pisa (stage) modes in pisa_examples/pisa_modes.ipynb (reflects my understanding, felt like the prior version was a bit too brief)

[LeanderFischer]

Hey, thanks a lot for the detailed checks and additions! Looks very good to me and definitely enhances the documentation 🔥 Since I set up a workflow to automatically create the docu recently, that will immediately go in, once merged.

[thehrh]

Cool, I can see it there already.