Port merge-user-metadata to augur curate

[joverlee521]

Description of proposed changes

Porting over merge-user-metadata from nextstrain/ingest to augur curate apply-record-annotations.

Includes a functional change to skip annotations for fields that do not exist in the record because it's hard to ensure that the new field gets added across all records that are streamed through the command.

This is a deviation from the original nextstrain/ingest script, but I think a necessary one to avoid bugs in the final output metadata.

Related issue(s)

Resolves https://github.com/nextstrain/augur/issues/1482

Checklist

• [x] Checks pass
• [x] If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR

[codecov[bot]]

Codecov Report

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

Project coverage is 69.28%. Comparing base (0adfe3d) to head (8ee9d82).

:exclamation: Current head 8ee9d82 differs from pull request most recent head 63744c6

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1495 +/- ## ========================================== + Coverage 69.15% 69.28% +0.13% ========================================== Files 70 71 +1 Lines 7694 7727 +33 Branches 1887 1895 +8 ========================================== + Hits 5321 5354 +33 Misses 2087 2087 Partials 286 286 ```

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