Adapt to new modular structure

[f-hafner]

pipeline.sh will not work as-is because calling a python script in a sub-directory, but loading a module that is not in that subdirectory will fail.
To fix: execute the scripts as modules, like this:

1. add a file __init__.py to all directories where there is a python script
2. in the pipeline, adjust the code for calling scripts from "python3 /some/path/script.py" to "python3 -m some.path.script"

See also https://peps.python.org/pep-0338/