Dear Dieter,
if you don’t run services other than BaseX, I would recommend you to check out the ZIP version of BaseX [1], which already includes the Jetty web server and some startup scripts [2], and which will ensure that your web application will find all relevants directories. We even think about removing the WAR distribution from our download page, as it required too much manual interventions. Some more information is given on our Wiki page on web applications, which also describes the options in the jetty.xml and web.xml files [3].
This may hopefully give you some answers on your questions; if you want to know more, please don’t hesitate and ask again,
Best, Christian
[1] http://basex.org/products/download/all-downloads/ [2] http://docs.basex.org/wiki/Startup#BaseX_HTTP_Server [3] http://docs.basex.org/wiki/Web_Application