Update (indistinguishable) protein groups when filtering protein identifications (fixes #748)

This was achieved by adding a method `IDFilter::updateProteinGroups`, which is now used in the IDFilter TOPP tool. See also the discussion [here](https://github.com/OpenMS/OpenMS/pull/1027#issuecomment-63799619).

Also includes a small change to the conversion of protXML to idXML, in order to avoid problems when filtering proteins in a conversion result.

In addition, all methods of the "IDFilter" class (not the TOPP tool) have been made static, since the class doesn't have any "state" anyway.