remote/s3 should instantiate its own MimeTypes instance

[joverlee521]

Originally from @tsibley in https://github.com/nextstrain/cli/pull/330#discussion_r1396150186

This addition is just fine, but seeing it and the existing additions above it reminds me that this module should probably be instantiating its own MimeTypes instance and modifying that rather than modifying the shared process-global instance.