Right now I have N files, each of which contains "pod" + "code". To combine them I just use cat.

Moving the pod away from the code feels like a bad idea.

Keep pod however you want, but don't deploy pod, but don't ship pod, but don't give the end user pod he doesn't care about, don't pack the pod that isn't meant for end user, strip it for deployment, strip it for packing, strip it don't ship it

When I'm using http://cpanmin.us/ I don't care about the modules it uses