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Improve CLI logging

Alf Eaton requested to merge 51-cli-logging into master

Closes #51

The aim was to asyncify as much as possible of pubsweet-cli, so that logging could be added between each await step.

This also moves package.json and the config files into initial-app rather than generating them from a string.

The .env file for an environment is now also generated when generating the database (i.e. running pubsweet setupdb …) - this could be made more explicit, but is better than the previous situation where the env file was only generated when generating the app.

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