notify user if a specified option is overruled, fix python test

Merged Gerhard Raven requested to merge improve-diagnostic into master
  1. notify user if the specified 'input_stream' is ignored - and do not specify a stream in one of the tests that ends up being ignored.
  2. fix the python test which runs multiple configurations inside a single process by resetting the global 'identity' registry before each test

Goes with LHCb!4116 (merged)

Edited by Gerhard Raven

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