SYSTEM TESTS: fix tests

[davidkeymer]

Modify run script to upgrade stock configurations (after copying to standard location) before running tests.

[davidkeymer]

Pull requests:

Upgrade script
System Tests

[John-Holt-Tessella]

I am not convinced this is the way to handle this sorry. Having thought about it harder this means that any database upgrade gets applied every time, I don't think this is good. Will set up a slightly different workflow for now until you are back to discuss.