feat!: enhance annotator CLI options

[jsstevenson]

• Make the input VCF path an argument rather than an option. I think this better matches the intent of the tool (and it was the only required option, so might as well make it an arg, right?). Left it at nargs=1 but I think there's a case for making it nargs=-1... but going 1 -> -1 wouldn't be a breaking change imo so I think it's fine to put that decision off.
• pathlike args should be click.Path/pathlib.Path. Add additional configurations, like the input file must exist and the output files must be writable. Didn't make changes further up the stack because I wanted to confine this PR to just the Click interface.
• remove some superfluous/inactive configs
• Touch up help text