The reason the .env file was not in the repo was so it wouldn't overwrite the local copy in an installation, losing usernames and passwords.
In the effort to make IoTa work 'out of the box' this was changed so the .env file became a runnable default.
This is too dangerous for production use so see if there is another way to work around this. Probably modifying run.sh to check for the file and copy it from config if it doesn't exist is the easiest way.
The reason the .env file was not in the repo was so it wouldn't overwrite the local copy in an installation, losing usernames and passwords.
In the effort to make IoTa work 'out of the box' this was changed so the .env file became a runnable default.
This is too dangerous for production use so see if there is another way to work around this. Probably modifying run.sh to check for the file and copy it from config if it doesn't exist is the easiest way.