I might be missing something, but before trying to duplicate the 99% of identical files, are you sure you are using environment variables such as PATH and PERL5LIB environment variables to full advantage, i.e. to define the runtime priorities for multiple directories?
Free your mind
Re: [OT] Best Use of Subversion Branches in Perl Development
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The idea of having a developer branch (or sandbox or whatever - depending on your particular version control metaphor of choice) is to have a copy of everything so you can tweak to your heart's content rather without the risk of messing somebody else's work up.
In any decent system branches are cheap since they only track changes to the files you tweak rather than duplicating them.