Yeah I suppose that wasn't so much a migration guide, as a case study. Suppose to demonstrate how easy it can be to use apm in an existing project, rather than a definitive guide on all possible scenarios. In that case we did restructure a few things but that was to clean up the structure that had gotten a little messy. (ANE's in multiple folders etc).
The deploy options aren't really documented currently, but they are listed in the project definition spec
apm really is hoped to sit alongside your existing structure as much as possible. Probably the biggest restriction is that the ane's from packages are all in one directory, which may be different to how some people have done it in the past.
If there is something missing or requiring more configuration please let us know 🙂