Use Foreman to manage environment variables in dev environment

Instead of pinning environment variables to `run.sh`, this allows them to be defined in a separate `.env` file and loaded at the run-time. Foreman will use `Procfile` to start the app.

Also, this PR contains few cosmetic changes:
* Organisation of Dockerfile.
* Updates the README.
* Adds a `update.sh` script to run update tasks (sorry, I couldn't actually test this as I was too lazy to generate secrets).