I just started to work through your lists. You added some glyphs that I think are not needed.
e.g:
The first one has the unicode 06BF, but the other three are not encoded. So I think you don't need a glyph for them. What you need is to decompose the glyph into tcheh-ar and dotabove-ar in the ccmp feature like this:
sub tchehDot-ar by tcheh-ar dotabove-ar;
I will see if I can add the ccmp substitutions automatically.
Mr. George my eyes crossed when I was working on this file and, I have to re-arrange and classify Arabic (typefaces) , but still there is a lot needs to re-adjust and classification
Sir George
All the arabic Glyphs which are located within the property Discretionary Ligatures do not need to decompose because they contain a new form is completely different from the basic shape of his
Sir George
There are important programmatic codes should work automatically in Glyphs App rather than add them manually every time
required ligatures
sub alef-ar lam-ar.init alef-ar.fina by alef_lam_alef-ar;
sub alef-ar lam-ar.init alefHamzaabove-ar.fina by alef_lam_alefHamzaabove-ar;
sub alef-ar lam-ar.init alef-ar.fina by alef_lam_alef-ar;
sub alef-ar lam-ar.init alefHamzabelow-ar.fina by alef_lam_alefHamzabelow-ar;
discretionary ligatures
sub alef-ar lam-ar.init by alef_lam-ar.init;
Sir George
Is there a possibility to adjust the marks in Glyphs, once the key press Control + U?
Away so that the mark on the glyph automatically by a certain amount as in the picture
This will make the process of adjusting the marks that quick, especially the arabic fonts depends entirely on the marks