Yesterday I published a new version of markdown-doclet which fixes the issue of using custom Taglets, which was raised by a user report.
I also spent some time looking into a few of the other more difficult problems I’ve been aware of for a while, but wasn’t able to make much progress in the little time I had available.
Have been extremely busy the last couple of months and so will have to shelve those things until a later date.
However should you want to use custom Taglets with markdown-doclet, it should now be possible.
Interestingly enough, the user report was in reference to ditaa which I wasn’t aware of until now, but is a pretty cool concept. Definitely worth checking out if you like making ascii diagrams (who doesn’t?) 
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This is just what I was looking for. I haven’t been able to try it out yet but I’m very excited about the ability to replace HTML with Markdown in my JavaDoc. I wish the standard JDK incorporated this..
Also that ditaa site looks awesome.