Refactor io/add auspice output

[rneher]

The output directory now contains a json file that is compatible with auspice.us. Both time scaled phylogenies and ancestral inferences can now be visualized and explored using auspice. Available colorings are "Date", "Genotype", "Branch support", and "Excluded". The first two work exactly like standard nextstrain/auspice viz.

• "Excluded" is a coloring that indicates whether this leaf was flagged by the clock-filter. The date constraints of the excluded leafs are ignored.
• "Branch Support" colors branches by 1 minus the inverse of the exponential of the number of mutations on the branch. This approximates a bootstrap support value (for closely related strains) and in particular will mark all branches without mutation support (introduced during polytomy resolution) as having no support.

In addition, this PR moves many functions that do IO for command line wrappers into a separate file CLI_io.py.