As mentioned by Rob in from the Q&A
If the folder itself has not been included in the project the plugin doesn't seem to pick up the folder not being included along with the files inside. It would be useful if it did this or if there was an option for it, although I can also see how this might generate a lot of 'errors' that people didn't really want to see. Thanks for your help.
As mentioned by Rob in from the Q&A