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ingest: Always provide default config values
Part of work to update this repo to match the pathogen-repo-template. Always provide default config values that can then easily be overridden with --configfiles/--config options. This makes it simpler to change a subset of config values or extend the default configs. Renames the config/ to defaults/ to reflect this change. Match changes in pathogen-repo-template in nextstrain/pathogen-repo-guide#27
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