If you want to use unpacked WARs, you should perform this as part of your deployment. The default for standalone Tomcat is to unpack a WAR but is not the only way it will operate.
Under the J2EE specs, it is not necessary to unpack a WAR and many app servers do not do this - that is, they do not materialise the entire WAR file structure to the local file system, particularly if the WAR is stored in a DB, stored on a remote file system or accessed via a URL.
Since I assume that the class methods are invoked from a servlet, you might consider redesigning so the servlet passes a context reference so you can obtain a file in the WAR via getResourceAsStream("..."). This would also make your application more easily portable since you are not reliant on unpacked WARs.
The JVM uses the JBoss bin directory as the starting reference as this is the directory in which the JVM was started.
I think those are the set of options available.