I've exchanged a few e-mails yesterday and today with someone who was having trouble installing
blojsom under JRun. The error message that he sent me was related to log4j. So, I googled for
jrun WEB-INF/lib and one of the hits on there was
getting JIRA to run under JRun 4. The error message and symptoms seem to be exactly what this person was seeing with blojsom. Of note,
"JRun does not follow the servlet spec when it comes to classloaders, and its own libraries (in $JRUN/lib/) will be loaded before those in WEB-INF/lib." I don't know what the current state of affairs with JRun 4 is or if there have been updates that address this issue, but the /WEB-INF/lib directory is there for a reason folks.
To the developers of JRun: Make this easy on your customers who are paying $899 for your software and implement the Servlet/JSP specification correctly. It's been out for awhile and you've had ample time to get it right. Otherwise, do what BEA did with Weblogic and offer the "Prefer WEB-INF classes" option!
Oh, and thanks to the Atlassian folks for the "help"