reorg/run.sh: does not dump settings by default.

Introduces behavioural change in run.sh

- Deprecates the --no-create-run-settings: run_settings.yml is only
  created if --create-run-settings is passed explicitly

run.sh returns proper exit code

Change-Id: I2b21aa54a7db74b1cb2ad3c7e881c6542bc1b8e0