How to reproduce the bug:
1) Download some example apps, for example

git clone https://github.com/glassfish/javaee7-examples example-apps
cd example-apps

2) run forge

forge

3) Run the windup
windup-migrate-app --input jms-websockets-with-cdi/ --output output

The output ends with:

**INFO** Executing Rules: :[Java] [822/833] ...
**INFO** Executing Rules: :PRE_REPORT_GENERATION - org.jboss.windup.reporting:windup-reporting.CreateApplicationReportIndexRuleProvider [Uncategorized] [823/833] ...
**ERROR** Error while executing 'Windup Migrate App'
**ERROR** Error encountered while evaluating rule: .addRule().when(org.jboss.windup.config.query.Query@7141f363).perform(org.jboss.windup.config.operation.Iteration@20d222ac)
From: org.jboss.windup.reporting.rules.CreateApplicationReportIndexRuleProvider
Defined in: org.jboss.windup.reporting.rules.CreateApplicationReportIndexRuleProvider.getConfiguration(CreateApplicationReportIndexRuleProvider.java:54)
**INFO** (type "export VERBOSE=true" to enable stack traces)
**ERROR** Error encountered while evaluating rule: .addRule().when(org.jboss.windup.config.query.Query@7141f363).perform(org.jboss.windup.config.operation.Iteration@20d222ac)
From: org.jboss.windup.reporting.rules.CreateApplicationReportIndexRuleProvider
Defined in: org.jboss.windup.reporting.rules.CreateApplicationReportIndexRuleProvider.getConfiguration(CreateApplicationReportIndexRuleProvider.java:54)

The exception that is nested inside tells, that there is no project found in the folder jms-websockets-with-cdi.