Refs #9343 Add unit tests for indirect common script.
Refs #9343 Do some re-factoring.
Refs #9343 Checkpointing work so far
Refs #9343 Refactor function to use existing code
Refs #9343 Remove unused function.

Searched code base and it appears this is no longer needed anywhere.
Refs #9343 Remove unused argument.

This option does nothing and is not used, so should be removed.
Refs #9343 Refactor extract functions.
Refs #9343 Checkpointing work.
Refs #9343 Apply stashed changes.
Refs #9343 Adding more tests.
Refs #9343 Updating documentation and removing debug statements.
Merge branch 'feature/9343_indirect_common_script_tests' into develop

Conflicts:
	Code/Mantid/scripts/CMakeLists.txt