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In a recent blog post, Kai complained about various existing tools for marking up email in HTML. He also asked for pointers to other tools. Since he didn't specify good tools :-), I took the opportunity to promote my work in progress plugin for ikiwiki to do that very thing.
When asked about demo sites, I realized that my blog doesn't actually use threaded comments, yet, so made a poor demo.
The basic idea is to use the Email::Thread perl module to get a forest of thread trees, and then walk those generating output.
I think it would be fairly easy to make a some kind of mutt-like index using the essentially same tree walking code. Not that I'm volunteering immediately mind you, I have to replys to comments on my blog working (which is the main place I use this plugin right now).
For a project involving ikiwiki. I am thinking about the right way (or at least a reasonable way) to encode things into email address. At the moment I am leaning towards a hybrid quoted printable/base64 style approach.
You can have a look at my current implementation of a module Convert::YText to do this conversion.