-The tree evaluation functions (-f e/-f E) now also generate a file that contains all
 trees with branch lengths that were optimized.
-They are printed in the same order as the input trees and the code can be easily re-started,
 that is, the final evaluation run (in case of re-starts) will print out all likelihoods and all
 trees in newick format to the above file because this data is being checkpointed.