e.g. MantidConfiguration is replaced only if a user have not touched it.

Though testing and running as user is still needed

a particular user from command line. Not tested

ISISDirecInelasticConfig.py is used by BuildMantidConfig script and this script has to be changed to use new ISISDirecInelasticConfig.py interface. The change allows to change script independently of each other as ISISDirecInelasticConfig.py supports both old and new interface.

looks complicated

and unit tests for it. All seems work fine.

and fixed all previous unit tests, affected by changes UserProperties

and better logic behind replacing sample file.

and unit test for it