Suppress remaining errors from copyright script

- Add a mechanism to the script that allows it to be used only for
  uncrustification, but not for copyright checking for certain files.
- Use the mechanism to suppress copyright checking for thread_mpi files.
  It's somewhat unclear whether we should just prepend the Gromacs
  copyright to these files and get rid of this exception, or whether we
  still are planning to maintain the library separately.  But until that
  is clear, this keeps the script quiet, and the copyright headers need
  to be manually maintained if desired.
- Suppress a few files that don't have any copyright header.
- Add copyright header to two source files that were still missing it.

With these changes, running admin/copyright.py on all files indicated by
.gitattributes only produces messages about outdated copyright years
(which it should, for files that have not been modified this year).

Part of #818.

Change-Id: I2cb09b2b30e782244c16faf02625d405dac642b6