Here are directions for converting a markdown/multimarkdown formatted text manuscript into a Microsoft Word document (unfortunately still a preferred format for submission to many journals). These directions will focus on turning bibtex citekeys (if you are using BibDesk or similar for references and bibliography management) from the [#citekey]
format in multimarkdown to the \cite{citekey}
format for use with BibDesk.app and BibDeskToWord.app to
This will use the Multimarkdown command line tool (mmd2odf) to create a flat open office document .fodt text file. Multimarkdown must be installed on your system. Alternatively pandoc can be used for this, but pandoc doesn't handle the nice multimarkdown table format as well and graphics can be messed up in resulting open office document .odt file.
Note on use of fodt files in OpenOffice:
>LibreOffice can open these Flat OpenDocument files by defaul