Hello 
I am stuck with a GSUB lookup type Ligature substitution (mixed base and mark substitution), I want to show the anchored marks (not to include them in the glyph) because I want to color them later, how can I force the anchored marks to be shown after applying the feature?.
Please help me, and here’s a photo explaining my problem:
It is probably easiest to color the marks, otherwise you need to add color marks to your glyph1.
Thank for your reaction, the problem is that this is not normal ligature substitution, it is BASE+MARK one, so OT forces the marks to disappear, that’s my problem.
We might be able to help if you can provide a sample font project that illustrates the problem with just a couple of glyphs.
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Thank you @ErwinDenissen for your reply, here’s the font with minimal glyphs:
Please notice that I didn’t use the Ligature (liga) feature I only used Contextual Alternates (calt) because in my case this glyph ligature occurs only with specific marks on the two combined letters.
So what I want is to have the marks shown on the custom glyph as FC or OT force them to disappear after adding the CALT feature (The marks are shown very well in the case of LIGA feature).
I have a children book that I will color all the marks with InDesign built-in GREP style, the coloring inside FC is well impossible but InDesign doesn’t support CPAL/COLR 
Here’s a photo with more details:
Why don’t you export with OT-SVG support?
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Sadly the diacritics and composite glyphs of Arabic doesn’t work well and get corrupted in InDesign after exporting to OT-SVG font 