#881 Cleanup box writing

And of course once you start moving things you run into all kinds of dark and dusty corners 😄
First step, cleaning the walkers generation and Box writing.

• 1st part of the commits is taking very small steps in unifying walker generation code.
• Eventually that ends with writing the result through Box.
• Extending Box with allowing relative paths and deprecating the single path method.
• Next is then fixing all the deprecated calls. If didn't bother with a full solution in cif2plc.
• Finally remove the deprecated method.

I ran the walkers and emf code/doc generators of CIF and had no changes in the output.

Addresses #881