[enhancement] better consistency in how output model filenames are formatted

Previously the model_filename_format config option was only used for outputting the final version of the net after the last epoch. Now it's used during all stages of training so that the format is consistent whether it's the best net, the last net, or other checkpoints that we might define along the way.

also adds a --checkpoint option to dnadna predict such that when passing a training config file, it allows specifying the checkpoint to load the net from (with 'best' by default).

This came up while working on #53 (closed).