If "we" like to leave the original PB API (folder) alone, and non-frequently update the JR API collection, it feels best to delete the latter folder content before adding the new files from Jose's forum.
In such case it would be desireable to have the option to add an additional folder for other includes, for ease of maintainance and better control/oversight.
An optional way to achive this would be to use the "Jose Roca's Include Path" string from the Environment Options as a base and allow FF to include any subfolders for includes.