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Use a separate app instance for migrations

Hugo Kerstens requested to merge 694-separate-migrations-app into master

This MR:

  • Splits the app factory in three:
    • One function to initialize the app only with the config
    • One factory for the main app used for the api using wsgi
    • One factory for the app only used for migrations, which has no side-effects
  • Configures package.json to use the correct app for migration commands

Closes #694

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