In Jenkins, you observe that CommandLine recognizes both the reference project as well as the main project, and brings in the project workspace. However, the Jenkins/CI workspace does not have the sources for the main project, only the reference project. You also notice that there is a no such file exception that originates from the CommandLine.
The issues are very misleading in their error messaging as well as the symptoms that are seen in regards to Jenkins configuration, Maven, and CI Builder. The root cause of this issue was the URL for Nexus within the CommandLine config.ini file: the port was erroneously left as localhost:8080/nexus instead of localhost:8081/nexus. Verify in the config.ini that all other settings are correct for the CommandLine.