Update PinkPill.pm

Added functionality to include libraries at link time.
Update PinkPill.pm

Lots of tweaks through out the file to try to use the Perl File library as it provides a lot of cross platform support already.
fixed some of the issues that these changes have created, also cleaned up some of the formating.
list of files is no longer being generated correctly, I suspet 'catfile' is being used incorectly.
ensured all changes are working correctly. Ready to merge