My solution turned out to be correct: Despite of what the API says the editor folders are completely ignored when building. So luckily Aaron has implemented a way to solve this.
Upgrade instructions :
1) Create a new project.
2) Import aaron's package
3) open any test scene and select the A* gameObject.
4) Press the button to restructuate for use with javascript
5) Import PlayMaker
6) Import the new package in these attachments
7) Import everything else from your old package
Change the object types of your variables (eg. from FsmPathfinding/FsmNode to FsmNode)
and yes, I did try to keep the structure... but there seems to be no way whatsoever to assign namespaces to javascripts, at least not in a way for them to show up in a subcategory in PlayMaker. And I tried for hours... :S
There are also some new updates and added actions, like get and set path info and AstarPath. Likely more but I'm too tired to check them right now.
Also, this will likely not be the last time you guys will have to update the object types of the variables. I fully intend to turn them back into FsmPathfinding/XXX s , just because without a category I find it very hard to look at.
Hope this works for you too.