The wsdl2java Ant task provided by Axis2 does not seem to resolve given pathnames against Ant's basedir property (as Ant tasks are supposed to (or, at least as built-in Ant tasks actually do).)
I have seen this for the wsdlFilename and output attributes, but presumably any other pathname attributes also have the problem.
To see the problem:
1. Create an Ant build.xml file containing a <wsdl2java> element whose wsdlFileName attribute refers to a WSDL file using a relative pathname (e.g., "x.wsdl" (as opposed to "/home/user/a/b/x.wsdl")) that works when you invoke Ant with your working directory set to the directory containing build.xml (e.g., when "ant -f build.xml" works).
2. Then change your working directory to some other directory and run Ant on the same file (using Ant's -f option to point Ant to the build file). The expected symptom is that wsdl2java will no longer find the WSDL file. The absolute pathname printed in the error message should confirm that wsdl2java is looking relative to the current working directory rather than relative to the Ant project's base directory (which defaults to the directory containing the build.xml file).
(See http://ant.apache.org/manual/using.html#project for information on the basedir attribute and some information on the base directory. Also, see mentions of "basedir" in http://ant.apache.org/manual/develop.html.)