need better control over what files are created/overwritten

[rdkibler]

the .gb outputs for separate genes are great, but the order.dna.fasta file is not great for the times when you need to re-run a selection of optimizations. In that case, the entire order.dna.fasta file gets overwritten

a better solution might be to write an order_{name}.fasta for each gene and have order.dna.fasta be the cat of all the order_{name}.fasta, or dont' write the order.dna.fasta at all

Also consider overwrite protection