Hi Alex,
Is there a backward/forward compatible way of encoding references?
The standard EMF way to encode references is still possible.
As long as you store your model in a single file you have all the possibilities.
We decided to define a strict scope (one folder) and name based references (without the file name) to allow extendibility: Multiple files can be copied to one folder and build one logical model.
The AMALTHEA examples (Wizard new... > examples... > AMALTHEA) are up to date. Take a look at the xml content to see further reference strings.
In general: If you have standard names (no blanks, no special characters) you can simply build references to e.g. a label as
NameOfTheLabel + "?type=sw.Label"
Regards,
Harald