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Multi configuration (#123)

* Removed config dict option

Removed config dict option from Pipeline() as it's never used.
Supporting config dict in the context of the new config file system
supporting multiple profiles would not be a good use of time.

* Outline profile-based config

* Multiple configurations added.

* Updated InstrumentUtils() based on feedback

Unittests need updating

* Additional unittests for InstrumentUtils()

* Updates based on feedback

* bugfix

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