Replace the `pre-nn` and `pre-nn-edges` by the `MLPEncoder`

Replace the `pre-nn` and `pre-nn-edges` by the `MLPEncoder`. Also allow `pre-nn-graph` and `pre-nn-atten` (I think this would come naturally).

In `MLPEncoder`, replace the use of the `MLP` class by the `FeedForwardNN` class for more options.