I am trying to deploy a working application war(exploded) into jboss 5.0.1, but it is getting failed and I think there is some problem with setting classpath for org/apache/catalina/logger/Filelogger.class.
That class is not provided by JBoss AS. You have two options. One is to replace the use of the Catalina logger with commons logging (that is what I would do). The other is to repackage the Catalina logger into a JAR file and provide it with your app. This might take some doing to get the right set of classes. Also, I looked in Tomcat 6.0.18 and could not find this class.