The axis jar files need to go into tomcat:

Copy all the jar files from lib into a new folder packages/tomcat/sharedlibs

Edit tomcat's packages/conf/catalina.properties
Set the shared.loader property:

shared.loader=${catalina.home}/sharedlibs/*.jar

To install pharos:
ant configure: generates config files
ant compile: compiles code
ant install: copies files into greenstone3 area