Config based Augur commands

Update existing Augur commands to take YAML config options, similar to the new `augur subsample` command. This will allow us to create "generic" workflows that call Augur commands without hardcoded CLI options or Snakemake functions to change options based config params. Common commands used in phylo workflows that we should consider updating: - [ ] mask - [ ] align - [ ] tree - [ ] refine - [ ] ancestral - [ ] translate - [ ] traits `augur export` already uses a mix of CLI options and the Auspice config JSON. We should consider if we'd want to consolidate these with a YAML config or if the `export` command should be left as-is since it needs to be tailored per workflow anyways (i.e. input node data JSONs depend on upstream rules in workflow).