I stumbled upon an additional problem, not sure if this is related or not, but posting it here. I've upgraded to JBoss tool 3.2 beta 2 since the last post. Still on Ubuntu 10.10, 64 bits, Eclipse 3.6.1.
Occasionally when I save a file in Eclipse while JBoss AS is running, e.g. save a single .xhtml file, this triggers the deployer to deploy hundreds of files again. The effect however is that not hundreds of files get deployed, but get deleted! This of course totally ruins the deployment. JBoss AS starts to complain about missing files, missing classes, or it reboots because WEB-INF/* has been touched, but then fails because WEB-INF is completely missing, etc.
In one word: major chaos.
After I saved my file, the following appeared in the Server Log view:
2665 files modified in module my_main_web
No publisher found for module DeletedModule[saxon9.jar,org.eclipse.jst.jee.server:/binary:/home/my/eclipse36ee/workspace/my_main/my_main_web/libraries/saxon9.jar]
No publisher found for module DeletedModule[jxl.jar,org.eclipse.jst.jee.server:/binary:/home/my/eclipse36ee/workspace/my_main/my_main_web/libraries/jxl.jar]