Fix --keep-ext and add --include-ext

[danielballan]

Needs unit test. Tripped over this while focusing elsewhere, bookmarking this for later.

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Tested!

Checklist

• Add a Changelog entry
• Add the ticket number which this PR closes to the comment section

[danielballan]

• Address comment in line
• Extend approach to tiled serve directory
• Smoke test

[danielballan]

Codecov cannot detect the coverage happening in a subprocess.

One build failed on an unrelated test. Must be a (rarely) flaky test.

FAILED tests/test_authentication.py::test_refresh_transparent[postgres_uri] - tiled.client.utils.ClientError: 401: Access token has expired. Refresh token. http://local-tiled-app/api/v1/metadata/A1