I was briefly involved in a GitHub discussion that happened before the fork but I think I got the reason why. People (well, me in that case) were asking for more fine grained options like per project instructions, and the Cline author's response was basically "not interested in the added complexity but feel free to fork". So somebody did.
Although I think Cline did eventually add some of the requested options.
Although I think Cline did eventually add some of the requested options.