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> But I don't know what are you going to do with the combining accent
> appearing after the letter.

Three possibilities occur to me.

1) make every character active and look ahead to see if it is being
   followed by a combining char.
   This is possible and fun to code in TeX but I don't really think it
   is a long term stable solution.

2) use perl (or anything else) to detect all combining characters
   and replace them by some command placed before the base.
   This is quick and easy to arrange, but if you are having a perl
   pre-pass before TeX, it may as well go further and decode the
   entire character stream into "latex internal form" ie 7bit ascii tex
   markup. In which case we may as well stay with that markup as latexs
   internal form.

3) use an underlying "tex" engine that understands unicode combining
   characters (and the unicode bidirectional algorithm) and other
   features of the unicode character properties. (and probably also xml
   document syntax as well)
   One day.

David