Merge HyPhy and fasttree subpipelines

[x] generate frequencies.json and turnover.json
[x] change file locations for evo history script
[x] add evo history script to pipeline
[x] change file locations for fubar script
[x] Add FUBAR script to generate rates.json
[x] rename subpipeline
[x] refactor main pipeline file
[x] remove old subpipeline
[x] add subdirectories for each subpipeline
[x] ensure new pipeline works for short amplicons, or at least have an option to disable parts that do not.
[x] update config file
[x] copynumbers in evo history script

veg / flea-pipeline