Does someone know how to solve this?
I also tried and failed with similar errors. I wish there was an update for this, it isn't up to date with the documentation. When you pull system build from git and run the setup script it won't let you select one template. You have to select fedora, debian and salt to get to the next screen where you can select ubuntu.
The same error happens for Qubes OS 3.2! Thus I can't build the latest qubes deb files for my xenial template that is now running with more and more old versions of core-agent etc. :-(
I wish I knew how to fix it... I tried the sugested "dpkg-source --commit" in various places but to no avail and I don't understand the build process good enough to figure out, what EXACTLY is going wrong here.