There are lots of good tools for working with markdown. The cd2md library makes it easy to convert a citedown document relying on a single repository to generic markdown. But many tools for working with collections of markdown source files either require or make it much easier for you if your source material is in a single, flat directory.
citedownmgr lets you organize citedown source in a normal directory hierarchy, and supports:
leanpub and bfdocsFor first release candidate:
Books.txt file for use with leanpub