This is still causing headaches with the latest version. After updating to 3301 today, I get 309 problems…
When selecting ‘update alignment’ and ‘new tab with affected glyphs’, we see every master appears twice, and the alignments are completely broken.
No matter what I try with rebuilding those glyphs, I can’t get auto-alignment to behave correctly. The mark ligatures are broken, they used to work with #exit and #entry anchors as we discussed before. Now those anchors are not being used (moving them has no effect).
It’s frustrating that every time I update Glyphs, I get a huge mess.