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There are 3 changes to the origin pegdown doclet:

Markdown Taglet

The possibility to write custom (markdown) taglets, not javadoc taglets.

Gist Taglet

Embedding a gist within your javadoc as (highlighted) code.

Markdown Corrections

It corrects/repair issues using the pegdown parser with javadoc. This is generalization of the ch.raffael.doclets.pegdown.Tags helper class.