Fix pre-initial cycle dependencies ignorance post restart

Closes #729

Fixes filtering of pre-initial cycle dependencies following a restart. I've deliberately kept that as a separate check here as we may want to use the db at a later date to retrieve the initial cycle time and/or add some protection against changing the initial cycle (i.e. use the old one and ignore the new one).

I've also added a test to ensure the pre-initial cycling behaviour persists following a restart.

N.B. this change has necessitated a change to the states checked by the existing restart tests - should be the final fix needed for #737, though shutdown arguments will likely need changing.