my first thought after reading this thread was, why not get a filelist of your project directory and match it against the regexes of your MANIFEST.SKIP.

My second thought was, there must be an CPAN-Module for that.

I've found and tried ExtUtils::Manifest

A quick test with your project and MANIFEST.SKIP file:

rpi-wiringpi-master$ perl -e 'use ExtUtils::Manifest qw(skipcheck); sk
+ipcheck;' 
Skipping .gitignore
Skipping docs/sketch/arduino.ino
...
[download]

hope it helps