Transform Devel::Cover::cover::Functions.pm into Devel::Cover::cover.

Transform functions into methods of class Devel::Cover::cover.  Move
declaration of defaults and function for processing command-line options to
Devel::Cover::cover::defaults.

Change calls to subroutines in bin/refactor_cover to method calls.

TODO: The -version and -launch options do not yet work.  POD not yet updated.
There do not yet exist unit tests for Devel::Cover::cover and
Devel::Cover::cover::Defaults.