Grouping no longer supports large protobuf netlist

Hi,
After this [commit](https://github.com/google-research/circuit_training/commit/d5e454e5bcd153a95d320f664af0d1b378aace7b), I see the grouping code no longer supports two smaller split protobuf netlists as input as mentioned [here](https://github.com/google-research/circuit_training/tree/main/circuit_training/grouping#note). So I can not run the latest grouping code for the large protobuf netlist after splitting it into smaller netlist using [split_proto_netlist_main.py](https://github.com/google-research/circuit_training/blob/main/circuit_training/grouping/split_proto_netlist_main.py).

Start by comparing the grouping behavior around commit d5e454e5bcd153a95d320f664af0d1b378aace7b and read the note in circuit_training/grouping. Reproduce the failure using split outputs from split_proto_netlist_main.py; the fix is complete when the latest grouping code accepts the two smaller protobuf netlists described there.

Written by the indexing model from the issue text.