AnalysisScopeReader will read the manifest file of jar file and add the Class-Path entries into scope, by default. However, the class-path specification is for use when executing Java applications via the "java -jar" command. It doesn't apply to webapps (WARs). Actually, FileNotfoundException will throw up when I use WALA to analyze some large-scale WARS.

And I am working on to solve this problem by adding some extra method into AnalysisScopeReader. When it is ready, I will create a PR.