After a bit of reading I've finally managed to build and deploy the latest SVN version of JBossWiki for those interested, my problem with eclipse/maven was solved after following that advice http://www-02.imixs.com/roller/ralphsjavablog/entry/eclipse_maven_install_from_runas
Now the Wiki is deployed as a portlet and the page appears correctly, however the URLs to the pages don't seem right.
Eg. the link to the main page is :
Ok, I reply to myself. Seems the FriendlyLinkPlugin is the culprit, I disabled it in the WikiTypes.xml config file and now the links work.
The permalink is still incorrect so I commented that too.