Maven JSTools Plugin does not work on multi module projects as the jsDir is not resolved against the module base but the parent base directory (one level to high).
I included a patch against the current snapshot version that works for me.
baseDir patch
Sorry, been very busy :-) I'll take a look at this as we'll make a new release very soon.
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baseDir patch
Sorry, been very busy :-) I'll take a look at this as we'll make a new release very soon.