The Mardown syntax is a lightweight markup language which allows to convert the syntax to HTML files. However this format is not really standardized and does not support several features which are necessary in a wiki, such as:
links to resources and files
inter-wiki links
Categories
The docJGenerator tool uses the Mediawiki syntax used for wikipedia articles (Mediawiki).
As for articles specified in XML, the parsing of Mediawiki files will escape non UTF8 characters by specifying the "escapeNonUTF8" option on the command-line or the configuration file.
Notes
^ You can't use both the Markdown syntax and the Mediawiki syntax
See also
Mediawiki markup: This article explains the supported Mediawiki markup