Fix issue in configuration loading

* Fixes an issue where the ConfigurationRegistry would overwrite
  the initial application configuration object.

Co-authored-by: Jiri Kuncar <jiri.kuncar@cern.ch>
Co-authored-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>
Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>