Preserve parfiles when copying them to the output folders

In !193 (merged) we started to explicitly write the parfiles ourselves to the output directory, because by overriding parameters we have to insert them in the correct TOML section.

This has a few drawbacks:

• ordering of the keys and sections is shuffeled
• formatting of the initial parfile is not preserved
• any comments are not preserved

The first point should be fixable with a PR to TOML.jl so that it can parse into OrderedDict. Not sure what to do about the others...