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I can see little thingies in the second rendition of Agacles (beside the upper case alpha and above the eta). My unicode table tells me those are respectively the Alpha with psili and the eta with perispomeni, whatever they are. So, if that is what you wanted, you have got it right. I don't see anything else with funny marks on the alpha page though.

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On the theta page, there are lots of marks: again my unicode table tells me these are additional goodies like dialytika, tonos, and varia. And the final sigma form is used in the right context.

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So, I guess on a typical linux installation that handles unicode right, I am seeing what you intended (I do not see it in the exact same font that you probably have on your machine, but as long as the unicode is right, people should be able to see it as long as they have one Greek unicode font on their machine). I will check from a mac sometime, but I am sure it works: I will post if it does not.