There is one large directory, called docs, with a lot of nested directories, some of which have 2 more levels of directories inside them, that I want to get rid of entirely. Running java -jar ~/bfg-1.12.15.jar --delete-folders docs
actually made the repo slightly larger, though it seemed to execute fine. It listed the dirty and modified commits, the changed objects, and logged a report.
Is the issue that it doesn't removed the nested directories, only the top level one? Can it remove things recursively?