(apologies for the double post, I was waiting for moderation)
I can't leave you a PM here, but I've submitted an untested
pull request on github to see if you'd be open to trying this out for us and possibly adding it to your code base. I don't have my wipy operational yet, so I have tons of print() statements in there to ensure the order of my ftp commands is correct.
It's basically a means (hopefully) to upload module folders into /lib/ not just modules packaged into single .py files inside /lib/. From what I've read, micropython should support this just fine.
I've also added a flag (which I have commented out) for a --noexp option for your script to operate by filtering out any commands which would use SD storage, etc..