Fix extant references to former GPL licensing

Some files did not have the copyright header I applied in 2012, so
I have re-applied that header as I would have then.

Some references remain in src/contrib and share/top/residues.dtd,
because I do not know whether they should change.

Change-Id: Ia80adc0c55ac1776297754a90cc0f8b5de7eae8f