Add parameter file version number and change scripts

[bwvdnbro]

Some code changes affect the parameter file: parameters become obsolete or get replaced by other parameters, new parameter blocks are added and sometimes have non-trivial default values... This makes (re)using old parameter files problematic in some cases.

The solution to this would be to keep track of the code version when writing a parameter file (especially when writing the parameters-usedvalues file). Then it would become possible to provide Python scripts that automatically update old parameter files whenever such changes occur.

[bwvdnbro]

Currently addressed by #63 that automatically converts deprecated parameters to their new values.