fixes #271
fixes #272

- consistent use of /usr/bin/env perl shebangs
- consistent use of 'use warnings;' in favor of perl -w
Merge #! fixes to misc/ scripts

Use "#!/usr/bin/env (perl|python)" throughout, to get the interpreter
from $PATH.  Use "use strict; use warnings;" in Perl scripts (this merge
commit also re-adds strict in novo2sam.pl).  Fixes #273.

(These small changes are not legally significant for copyright purposes,
so years in the copyright notices have not been updated.)