The default Hebrew list of Glyphs & Marks:
yodhiriq-hb, yodyodpatah-hb, shinshindot-hb, shinsindot-hb, shindageshshindot-hb, shindageshsindot-hb, alefpatah-hb, alefqamats-hb, betdagesh-hb, gimeldagesh-hb, daletdagesh-hb, hedagesh-hb, vavdagesh-hb, zayindagesh-hb, tetdagesh-hb, yoddagesh-hb, finalkafdagesh-hb, kafdagesh-hb, lameddagesh-hb, memdagesh-hb, nundagesh-hb, samekhdagesh-hb, finalpedagesh-hb, pedagesh-hb, tsadidagesh-hb, qofdagesh-hb, reshdagesh-hb, shindagesh-hb, tavdagesh-hb, vavholam-hb, betrafe-hb, kafrafe-hb, perafe-hb,
is not active as Compound glyphs after Export.
For example when typing: yod-hb + dagesh-hb the application does not refer to FB39 (yoddagesh-hb)
while testing on other fonts such as Adobe Hebrew it shows active in the Indesign/Type/Glyphs menu.
The following examples illustrate this issue:
Here … choosing: yoddagesh-hb indicates two separate glyph+mark:
My suspicion is that Glyphsapp is not compiling ccmp OT feature for Hebrew!