Master add flag convertor and fixes

As discussed in various meetings, it would be useful to have standardised conversion from old-to-new flags, at least for the most basic ones

This is a first attempt, so comments are welcomed. Please note that even with recent MRs improving the defaults for NewConfig, we use RecExCommon in many workflows and so we cannot rely on defaults - newconfig must match oldconfig.

As agreed, I also made mismatches a FATAL error (and throw an exception) to avoid having misconfigured new config overwriting correctly configured oldconfig.

Tagging a few people who might be interested: @ponyisi @goetz @mhodgkin @elmsheus @wlampl @fwinkl @tbold @tadej @nkoehler