Adjust more copyright headers

Replace old copyright headers with the new in files that have been moved
to the new module layout.  Adjust the script to handle the cases
encountered, and add some exclusions to the attributes.

Put best-guess estimates for the copyright years based on when the files
were created (if recently) and when they have been modified.  Unless
obvious that the file was created for 4.6 or otherwise recently, did not
trace back beyond the time the files were moved to their current
locations.

Files under directories moved as a whole from release-4-6
(legacyheaders, gmxlib etc.) have not been considered yet.

Part of #818.

Change-Id: Ida30498a97606ec652008299fc1652ca9609539e