Add instructions on adding subcommands

[victorlin]

It would be good to document the required functions and general patterns that subcommand files are expected to follow.

This is from a proposal in 48b0891. I omitted the "Docstring" section since that was based on other unmerged changes in the PR, but some parts (e.g. "each command must start with a module docstring") may still be relevant.

Writing a command

Functions

Each command must include a function register_parser(parent_subparsers, **kwargs). See the docstring of augur.argparse_.add_command_subparsers for more information.

If a command has sub-commands, those should be added with augur.argparse_.add_command_subparsers.

Most commands should define a run(args) function which serves as the indirect entrypoint from the CLI, where args is the value given back by argparse.ArgumentParser.parse_args(). If this function is not defined, the help output will be shown.