Not quite sure what you mean by packages. Are they JAR'ed or zipped in the lib?
Normally, you would expect the WARs to run normally - except for the fact that the WARs do not get unpacked. There might be slight changes that need to be made - such as using the JBoss datasource pools rather than the Tomcat datasource pools as they are not implemented.
Perhaps if you post the details of exact instances, that might make it easier to get to the problems and solutions. At the moment we're just flailing around in the dark answering general questions - which most probably is completely unhelpful for solving your problems.
For example I tried to install the axis example application which contains .jar files in the lib folder of the WEB-INF directory. For some reason if I create a war file by typing jar -cff axis.war * and deply this application. It does not see the .jar files I placed into the WEB-INF/lib directory. It does this with almost all of my applications. If I place the files into the /server/default/lib directory this works just fine. What I am asking is do I need to specify the .jar files somwhere in jboss for each individual application?
My Directory struction
------axis.jar (Classes not loading properly in JBoss)
Let me know if this makes any more sense?
OK. We're using the Axis RC2 in JBoss 3.2.0. As an aside, JBoss provides a JBoss.NET service that is a Wrapped Axis service. It allows you to deploy WSRs (Web Service aRchive) in JBoss. It is easier then to deploy a Web service in JBoss - but other commercial app servers have problems with a WSR.
WEB-INF/lib - axis.jar, axis.ant, commons-discovery.jar, commons-logging.jar, wsdl4j.jar, xmlParserAPIs.jar and xmlsec.jar.
WEB-INF - web.xml, jwsClasses directory, classes directory with examples, attachments directory and the
server-config.wsdd file (as well as those .lst files).
You probably should have the happyaxis.jsp to check everything is working.
Remember that you will need the support libraries as specified by the Axis installation guide. I put saaj.jar and jaxrpc.jar in the jbossweb-jetty.sar directory (you might need to put it in jbossweb-tomcat.sar or jbossweb-tomcat41.sar depending on your 3.2.x/4.x distribution - otherwise I hope you get the general intent for applying it to older distributions).
As I remember, the other support libraries should already be installed in JBoss in server/instance/lib - xalan.jar, mail.jar and that kind of thing.
happyaxis.jsp should be able to tell you the state of your Axis installation.
Hope that helps a bit as otherwise, you shouldn't have too many issues with Axis installation.