Hi @manuq, sorry for the slow progress here.
Rather than figuring out the right way to get this on the Endless infrastructure I have been looking into having it built on flathub.org, which seems like the appropriate place for apps like this.
The first step here will be to move io.atom.electron.BaseApp to being a project built on flathub, since flathub also seems like the appropriate place and they probably wouldn't want to retrieve the baseapp from Endless hosting. At the same time we should migrate it to freedesktop SDK v1.6. Should be easy.
The harder part is Sugarizer. I have adapted your work here, into a form where you feed a json file into flatpak-builder and it installs into /app, this is what flathub requires: https://github.com/dsd/org.sugarizer.Sugarizer
However flathub also requires that the build process doesn't use network access. Right now it runs "npm install" and downloads a whole bunch of stuff. I am planning to look into the new features of npm 5 which might help here (https://github.com/npm/npm/releases/tag/v5.0.0) or yarn (https://yarnpkg.com/blog/2016/11/24/offline-mirror/). I guess ultimately we will need to find an easy way to capture everything that "npm install" wants to download and convert that into entries in the flatpak-builder json file. If that process can be scripted or automated in part, it will help for future updates.
If you are interested in looking into this your help would be gratefully received!