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libsbml uses longs for functions like model.getSpecies(long n) or model.getReaction(long n). jsbml uses ints in these functions, requiring changing code. I would guess that it would be relatively straightforward to switch to using longs.
I have open a discussion on the jsbml development list (email@example.com) but it should not be a problem to change the method to use long, yes.
After some discussion, it seems we will not modify the current code but let the compatibility module handle that.