Remove export v1

[victorlin]

Prompted by #1262 (comment).

Description

export v2 (for Auspice v2) has been around for a while, and should be widely adopted at this point. There should no longer be a need to maintain export v1 in newer versions of Augur.

Tasks

• Add a deprecation warning to export v1. export v1: Add deprecation warning, remove --metadata-id-columns #1265
• Remove export v1.
• Move export v2 to export with a command line "redirect" in place. (maybe not necessary)

[joverlee521]

Noting that we still use export v1 for the private seasonal flu builds, which are visualized with a deprecated version of auspice.

[victorlin]

@joverlee521 that's good to know. Do you expect that those builds would benefit from newer features of Augur? Or can it also vendor its own version of Augur, similar to its current usage of Auspice?

It doesn't seem sensible to keep export v1 around just for one project, but I also realize that it's a project of our own lab...

[joverlee521]

Hmm, maybe we could vendor its own version of export v1 for that one rule only.
The rest of the workflow shares rules with the public flu builds which do benefit from newer features of Augur.

[jameshadfield]

Let's at least add the deprecation warning. It's good practice to leave things around for a while after the warning appears, so that'll give us plenty of time to decide what to do re: seasonal flu. In hindsight, having a sub-(sub-?)command wasn't one of my best ideas so perhaps we could explore things like making augur export the canonical export function, which behaves as augur export v2 currently does, but also have a (hidden) augur export v1 command.

[victorlin]

I started on this a while back with db54927...ec16b56 but it's probably stale now. James has started a new PR.