I was updating a font I haven’t touched in a while, when I noticed that many substututions are broken. After some debugging it turned out because mark glyphs were not classified as marks in GDEF table.
It looks like Glyphs is now not setting glyph classes for any glyphs without anchors, neither base nor mark glyphs.
See this test font New Font 2.glyphs (1.5 KB),
hamzaabove-ar has anchors, so both it and the composite
alefHamzaabove-ar have GDEF classes, but the rest of the glyphs don’t.