fix bug with reftree being rooted after pruning the preliminary mislabeled seqs before running the final EPA
fix bug with epa_use_heuristic=auto not working
- move branch length filter stuff to classify_util
- add branch length filter support in find_mislabels, BUT disabled for now
- do not use saved pre-optimized model for final EPA run on the pruned tree - led to anomalous placements