Refs #9204 - Make sure new settings object is cleared ...

... whenever the singleton is reset.

Also, slight change so that we only ever load the instrument once on
interface startup.
Refs #9204 - Workaround for bug in MaskDetectors ...

... so that things are no longer "flipped".
Refs #9204 - Explicitly raise "user file loaded" flag after startup.
Merge branch 'master' into feature/9204_allow_maskfile_commands_in_sans_isis_user_files

Conflicts:
	Code/Mantid/scripts/SANS/isis_reduction_steps.py

Refs #9204.
Merge branch 'feature/9204_allow_maskfile_commands_in_sans_isis_user_files' into develop