Hi stevieb,
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
...
hope it helps
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