Pull inputs in run(), not run_as_update()

For years, when invoking geomag-algorithms' update mechanism, inputs
were pulled and checked from the run_as_update() method inside the
Controller class. I never understood this. It seemed to break the
logic of the update mechanism if no inputs were available for the
current inteval/gap. This might even be the source of noted issues
where running back-filling scripts didn't behave as expected, and
those scripts needed to be run multiple times.

What's more, the run_as_update() method logically seems like the
most appropriate place to read *outputs* and check for gaps. Whereas
the run() method seems like the most appropriate place to read
inputs, apply algorithms, and write out outputs.

In any case, this change should not break any existing code. It
should only allow the update mechanism to complete, every time, and
as originally intended, rather than be short-circuited when input
data are missing for the current interval (but might be available
for previous intervals)..