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Out authors write in MultiMarkdown. This allows us, with a build file, a standard config & templates, to use Pandoc to produce neat clean ePub’s. We can then convert these using the Calibre command line utility into a MOBI for Kindle.

If necessary (as we do) you can re-write some bits of the ePub with XMLStarlet
e.g. for UUID or a cover for Kindle when converted.

Wrap all this up in a small script and you can go from the authors MultiMarkdown files into ePub and MOBI in a few minutes ;-)