dg1d:  allow parameter overriding on cmd line (!193)

Allows to use `main(parfile, "Mesh.n" => "1")` to override the value given in the parfile.

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To do this we
- parse the TOML file
- flatten the dict-of-dicts to a single dict with the keys joined by a `.`
- insert the parameters
- unflatten the dict to a dict-of-dicts
- write this to the output directory

Unfortunately, `TOML.jl` does not allow to parse into `OrderedDict`.
This causes the newly written parfiles to be messed up.
Furthermore, by manually re-writing the parfiles we also do not preserve any comments or formatting.