Hi

I've experienced all of these issues too. I've only got a solution for the first:

I'm using the ManifestSkip plugin and adding a MANIFEST.SKIP file with the patterns I want to ignore that aren't handled by PruneCruft.

A better solution would perhaps be to make a more configurable PruneCruft because like you, I looked into it and there didn't seem to be a way to override what it considers cruft.

I've adopted the same solution to you for the second one: adding package main; If I remember correctly this is so that the version number is added...

I've seen the third one but not recently. Maybe I'm not using PodVersion any more.

Still a Dist::Zilla beginner, but I find it very useful.

Cheers

FalseVinylShrub