Centralize --validation-mode and --skip-validation

[victorlin]

Description of proposed changes

Maintain consistency across all subcommands that take node data JSON as input.

Related issue(s)

• Fixes https://github.com/nextstrain/augur/issues/1635

Checklist

• [x] Automated checks pass
• [x] Check if you need to add a changelog message
• [x] Check if you need to add tests
• [x] Check if you need to update docs
• [x] Merge base PR https://github.com/nextstrain/augur/pull/1658

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 72.26%. Comparing base (ba370d9) to head (a6e045d). Report is 6 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1656 +/- ## ========================================== + Coverage 72.24% 72.26% +0.02% ========================================== Files 79 79 Lines 8268 8271 +3 Branches 1691 1691 ========================================== + Hits 5973 5977 +4 Misses 2009 2009 + Partials 286 285 -1 ```

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