@nix411 You should be able to just set the environment variables PRODIGY_BASIC_AUTH_USER and PRODIGY_BASIC_AUTH_PASS on the command line when you run Prodigy. For example:
export PRODIGY_BASIC_AUTH_USER=username
export PRODIGY_BASIC_AUTH_PASS=supersecret
prodigy ner.teach ... # etc.