Improvements to conf tool & config differences fixes

This MR is about getting closer between the rec-ex-common and newJO configs close. The most important thing is that it adds a file listing differently named components. It should be filled further. There are some minor settings fixes. The current difference is here: http://tbold.web.cern.ch/tbold/0427/only-differences.html Missing components are not listed.

@wlampl, @goetz - are differences like these in calo and ID expected? I guess not. Can you maybe try fixing some trivial ones?