All that is needed is one "protected" element in the file format that can be used by a script to store text strings. That one small addition would solve a bazillion problems with saving file specific settings like bone groups, or "animated constraints"... or anything else you can think of.
To make it even easier to use it could be part of the MohoDoc class:
Then it would be much easier to read in that string value from the AS file and parse it for whatever settings a tool or script might need. There could be many values saved to the same string for different scripts and tools.moho.document:userValue(string)
I find I am having to save either a separate text file (which is a pain) or save to the name of a bone or layer, which is also a pain but for different reasons since someone could delete the settings by deleting this special bone or layer.
-vern