Test Scenario update using Model.initialize()

[khaeru]

In message_ix, test_solve_legacy_scenario() tests that, among other things, a Scenario object which is missing certain items (sets, parameters) will have these added via a call to Model.initialize(), according to the scheme.

This was broken in #416 by 3bc8af6, but the tests within ixmp per set did not detect this.

Add a test for this behaviour that is expected downstream.