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2,030 changes: 2,030 additions & 0 deletions benchmarks/heck-relay/from-qfuerza/heck-relay_optimized.fld

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76 changes: 76 additions & 0 deletions benchmarks/heck-relay/from-qfuerza/paper_metrics.json
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145 changes: 145 additions & 0 deletions benchmarks/heck-relay/from-qfuerza/validation_results.json
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