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https://bugzilla.redhat.com/show_bug.cgi?id=799565
--- Comment #10 from Shriramana Sharma samjnaa@gmail.com 2012-03-09 11:43:21 EST --- I asked about this on Unicore list. One Microsoft engineer replied that they use reordering for this. I am guessing that they are treating the dot_reph character just like any other reph in any Indic script -- move it to the end of the syllable. The only difference is that Malayalam has a distinct character for this whereas in other scripts it is just RA + VIRAMA which is rendered as the reph.
So probably you can just treat it like the reph of other scripts. However, as Santosh says (and I already said) there will be a problem with the positioning.
One solution is to use akhanda ligatures as Santosh says but that is just a hack. The proper solution is to use GPOS. After all, that is what GPOS is for, isn't it? To position combining marks properly?
That said, I myself am not knowledgeable about all this GPOS-GSUB thing -- I'm more a Graphite person. So I leave it to you people to decide how to implement this.
I would only suggest that if you do use akhanda ligatures that you use composite glyphs instead of duplicating existing outlines. Would help in keeping the size of the font under check.