CLI Deploy - support collections key

[josephjclark]

As part of productionising Collections, we need to ensure that CLI deploy supports a top level collections key.

I don't think we need to do much here - it's just a simple singleton key/value in the yaml. We need to ensure there are no warnings and update the tests to make sure usage is tracked.

See OpenFn/lightning#2830 for the provisioning API requirements (basically we need to ensure compatibility with this).