Prepare for use of Dist::Zilla and some Perl best practices.

* remove NAME, Author, Copyright, and Methods sections from POD since they
are now generated by Dist::Zilla.
* replaced head2 for methods with method, attr or internal.
* add empty section for many undocumented internal methods.
* remove trailing whitespace and hard tabs to pass @BioPerl tests.
* use warnings and utf8.
* remove use of vars. Editing @ISA replaced with use parent, and $Version
is now generated automatically by Dist::Zilla during for release.
* replaced Makefile.PL with dist.ini.
* update the Changes file.
* move README for README.md
* update Citation since paper has since been published.
maint: update README.

* use markdown syntax.
* author is no longer the maintainer.
* remove "All rights reserved" since it makes no sense with the license.