sparse: move pruning of temporary includes into core This was our last method on the custom repo type, meaning we could remove that custom type and inline the 2 lines of code into reposetup(). As part of the move, instead of wrapping merge.update() from the sparse extension, we inline the function call. The ported function now no-ops if sparse isn't enabled, making it safe to always call. The call site in update() may not be the most appropriate. But it matches the previous behavior, which is the safest thing to do. It can be improved later.