I run the following command against the example EAR in the Windup source test-files/ directory:

windup-migrate-app --input /home/sgilda/GitRepos/windup/test-files/jee-example-app-1.0.0.ear --output /home/sgilda/temp/jee-example-app-1.0.0.ear-report --packages com.acme org.apache

Apparently it works if you run it without specifying packages.

This is the stack trace

**ERROR** Error while executing 'Windup Migrate App'
org.jboss.windup.util.exception.WindupException: Error encountered while evaluating rule: .addRule().when(Query.find(org.jboss.windup.rules.apps.java.model.JavaSourceFileModel).as(default)).perform(Iteration.over.perform(ParseJavaSource.and(org.jboss.windup.config.operation.IterationProgress@4ff3773e).and(Commit.every(10)))).withId("GeneratedID_w:apps:rules-java.AnalyzeJavaFilesRuleProvider_1")
From: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider
Defined in: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider.getConfiguration(AnalyzeJavaFilesRuleProvider.java:55)
at org.jboss.windup.config.RuleSubset.perform(RuleSubset.java:302)
at org.jboss.windup.exec.WindupProcessorImpl.execute(WindupProcessorImpl.java:91)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor$1.call(ClassLoaderInterceptor.java:87)
at org.jboss.forge.furnace.util.ClassLoaders.executeIn(ClassLoaders.java:42)
at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor.invoke(ClassLoaderInterceptor.java:103)
at org.jboss.windup.exec.WindupProcessorImpl_$$javassist_a41e6913-021a-4fac-986a-03124dbcb32c.execute(WindupProcessorImpl$$_javassist_a41e6913-021a-4fac-986a-03124dbcb32c.java)
at org.jboss.windup.ui.WindupCommand.execute(WindupCommand.java:318)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor$1.call(ClassLoaderInterceptor.java:87)
at org.jboss.forge.furnace.util.ClassLoaders.executeIn(ClassLoaders.java:42)
at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor.invoke(ClassLoaderInterceptor.java:103)
at org.jboss.windup.ui.WindupCommand_$$javassist_2effb943-c88a-4370-b771-6de6d3b490a9.execute(WindupCommand$$_javassist_2effb943-c88a-4370-b771-6de6d3b490a9.java)
at org.jboss.forge.addon.ui.impl.controller.SingleCommandControllerImpl.execute(SingleCommandControllerImpl.java:90)
at org.jboss.forge.addon.shell.aesh.CommandAdapter.execute(CommandAdapter.java:74)
at org.jboss.aesh.console.AeshConsoleImpl$AeshConsoleCallbackImpl.execute(AeshConsoleImpl.java:325)
at org.jboss.aesh.console.AeshProcess.run(AeshProcess.java:40)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at org.jboss.windup.rules.apps.java.service.WindupJavaConfigurationService.shouldScanPackage(WindupJavaConfigurationService.java:79)
at org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider$ParseSourceOperation.perform(AnalyzeJavaFilesRuleProvider.java:74)
at org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider$ParseSourceOperation.perform(AnalyzeJavaFilesRuleProvider.java:65)
at org.jboss.windup.config.operation.ruleelement.AbstractIterationOperation.perform(AbstractIterationOperation.java:67)
at org.jboss.windup.config.operation.GraphOperation.perform(GraphOperation.java:24)
at org.ocpsoft.rewrite.config.DefaultOperationBuilder$DefaultOperationBuilderInternal.perform(DefaultOperationBuilder.java:54)
at org.ocpsoft.rewrite.config.DefaultOperationBuilder$DefaultOperationBuilderInternal.perform(DefaultOperationBuilder.java:54)
at org.jboss.windup.config.operation.Iteration.perform(Iteration.java:237)
at org.jboss.windup.config.operation.Iteration.perform(Iteration.java:201)
at org.ocpsoft.rewrite.config.RuleBuilder.perform(RuleBuilder.java:168)
at org.jboss.windup.config.RuleSubset.perform(RuleSubset.java:234)
... 25 more
**ERROR** Error encountered while evaluating rule: .addRule().when(Query.find(org.jboss.windup.rules.apps.java.model.JavaSourceFileModel).as(default)).perform(Iteration.over.perform(ParseJavaSource.and(org.jboss.windup.config.operation.IterationProgress@4ff3773e).and(Commit.every(10)))).withId("GeneratedID_w:apps:rules-java.AnalyzeJavaFilesRuleProvider_1")
From: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider
Defined in: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider.getConfiguration(AnalyzeJavaFilesRuleProvider.java:55)