Tomcat 7 parallel deployment indicates versioned WARs by placing a ##VERSION suffix on the WAR file, e.g, my-app##001.war. (http://tomcat.apache.org/tomcat-7.0-doc/config/context.html#Parallel_deployment)
When deploying a JRuby on Rails packaged with Warbler, this results in a RackInitializationException, the root cause of which is a MalformedURLException thrown from line 1146 of org.jruby.runtime.load.LoadService.java. The malformed url looks like "jar:file:/opt/apache-tomcat-7.0.23/webapps/my-app##001/WEB-INF/lib/jruby-rack-1.1.2.jar!/vendor/rack-1.3.6/rack.rb".
That this is a malformed URL can be verified by simply passing the string to the constructor of java.net.URL: it will throw a MalformedURLException. Everything after the sharp symbol is being interpreted as a fragment rather than part of the file path.
One possible solution is to escape the sharp signs in a file path using standard URL escaping. '##' becomes '%23%23'. Experimentation confirms that Java is capable of parsing and reading from the example URL given above when it is escaped in this way.