Changing it is actually very easy to do so.�
Go to the link I gave you , scroll all the way down and you will find in the left side Project Summary , now underneath there is "Settings" click it.�
Now click to "Code locations"�
It will send you to the repositories.�
I would advise at this point to keep only the pharo 3 repository and remove the others but thats up to you. Now for each repo there is a Ignored files column , click on "edit ignored files", you can add files to be ignored or even entire folders. I would advise to keep folders only containing st files. That should solve the problem entirely and report 100% smalltalk.�
Give it a couple of days to update its statistics. �