It seams that the latest beandoc (0.8.1) still does not handle correctly a multiple subdirectories structure. As ziller, I have a project organized like this :
When running beandoc the above directory structure is correctly mapped in the output directory but the html files generated have bloken links; for instance :
output/a/context-a.xml.graph.html links to file:///output/a/a/context-a.xml.png (subdirectory is doubled)
output/a/context-a.xml.html links to the bean_local.gif as if they were in the same subdirectory (they are located in the output root directory)
links for bean references have also the subdirectory structure doubled.
BTW, nice job !