cli flags should override environmental variables

[imogenkinsman]

We use env vars to supplement our CLI, e.g. allowing users to scope all requests to a specific org without having to specify it in every request.

If a user specifies a flag that conflicts with an env var, the flag should take precedence over the env var.

1. Investigate where this is currently happening in the CLI.
2. Change all instances where env var takes precedence over flags.