I have following (simplified) structure:
WEB-INF/wsdl/test.wsdl
WEB-INF/schema/test/test.xsd
WEB-INF/schema/ebRS/rs.xsd

In test.wsdl is test.xsd imported (../schema/test/test.xsd)
In test.xsd is rs.xsd imported (../ebRS/rs.xsd)

Deployment failed with a FileNotFound Exception ( ..../wsdl/schema/ebRS/rs.xsd vs. i would expect: .../schema/ebRS/rs.xsd)
I tracked the problem down to WSDLFilePublisher.publishSchemaImports:
the resourcePath contains two slashes ( WEB-INF/wsdl//..schema/test/../ebRS/rs.xsd) before getting the resourceURL.
I think this caused the getMetaDataFileURL method to treat the '..' part after wsdl wrong. (when i correct the resourcePath value it works fine)

This failure occurs only if the schema files are not in wsdl directory branch.