[NOP] addendum to #1123

This pull request contains some additional cleanups for #1123.

 * move FeatureFinderSuperHirn code from header to cpp files
 * correct include order in files (1st OpenMS, then stl etc)
 * applied uncrustify to all files touched in #1123 

Please note that this pull request does not contain any substantial code changes, only cleanup and formatting.