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[RFD3] Feed MPNN real backbone atoms and the schema it validates
Verified signatureBuilds on #1. That PR made the diffusion path produce real backbones; this one makes the sequence design path usable. It contains #1's changes, so merging this alone lands both. ## MPNN never ran `MPNNModel.forward` built a flat dict and handed it to foundry, which reads everything from `network_input["input_features"]`. Every call died with `KeyError: 'input_features'`. Nesting it surfaced the rest of the contract: the network also validates `decode_type`, `causality_pattern`, `mask_for_loss`, `bias`, `pair_bias`, `symmetry_equivalence_group`, `symmetry_weight` and `repeat_sample_num`, and it wants a per-residue temperature rather than a scalar. The scalar settings now match `MPNN_PER_INPUT_INFERENCE_DEFAULTS` in foundry's `mpnn/utils/inference.py`; the optional conditioning keys are present as None, which is what the network checks for. ## MPNN was designing against invented geometry Even once it ran, the caller synthesised the backbone by adding three fixed offsets to every alph…046a4b1
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