Ah thank you for the clarification.
I think the problem is that the plugin is looking in the $WORKSPACE/build folder for the source files when they are actually in $WORKSPACE/src and $WORKSPACE/include. I have tried setting sourceDirectory: "${WORKSPACE}/src" but I am getting
'Removing source directory '${WORKSPACE}/src' - it has not been approved in Jenkins' global configuration.'
Adding it to the Warnings Next Generation Plugin Global Settings - Source Code Directories Absolute Path does not seem to help either. It seems like that path is for outside of the workspace but I would just like to point the plugin to an alternate folder in the workspace.
See discussion in https://gitter.im/jenkinsci/warnings-plugin?at=5ebe8f64863019312a5f8ebb