Refactoring and clean up

This issue is a collection of several smaller points.

Enhancing structure

• Clearly state which templates use which functionality (esp. f90/yaml namelist) -> wiki
• Homogenize naming of jobs/scripts/...
• Overwork namelist treatment: create all namelists first, symlink master namelist in run_icon, create namelists only when really necessary (i.e. not the same for each chunk)
• Check include file conf/common-KIT/art.yml for convenient overworking of includes (to reduce required work).

Enhancing files

• Homogenize output/debug level of templates
• Check scripts and yaml files for sufficient comments
• Check scripts for modularization/further use of functions
• In prepare_namelist_yaml.py (and possibly others): do not use global variables inside functions, instead create a namespace and pass that one on.
• Update Templates/Jobs to number of nodes.
• Python scripts: use logging functionality

Individual jobs/files

• Update wrappers to the enhanced job structures. This will be tackled fully in #58 (closed).
• SAMOA: run every few chunks to be able to interrupt a run on inconsistencies
• Check Pipelines for custom obsolete workarounds.
• Update README.
• Check #65 (closed).