Reading the instructions for bfg repo-cleaner, the work flow seems like:
However, then it is unclear to me whether you need to remove your own copy of the working directory and do a fresh clone, or whether you can just do a pull to get the clean repo/history? At the moment I am the only one who uses the repo.
You'd be better off doing a fresh clone, as your old working directory will have dirty history that you don't want to risk pushing back into your newly cleaned repo.