fix: broken Makefile continuation lines + benchmark status table

Three Makefile targets (bench-cluster-split, bench-expert-ablation,
bench-selectivity) had missing backslashes on continuation lines,
making them fail with "No rule to make target" or shell errors.

Also adds a Status column to the BENCHMARKING.md required benchmarks
table, marking all implemented benchmarks and adding the two missing
entries (expert ablation, multi-class triage).

Co-authored-by: OmX <noreply@omx.local>

Author: cschanhniem

Makefile

@@ -138,20 +138,20 @@ validate-scoring-phase3:
 		--out outputs/validate_scoring_report_phase3.json
 
 bench-cluster-split:
-	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench cluster-split 
-		--amp-csv examples/validation/known_amps.csv 
-		--decoy-csv examples/validation/random_background.csv 
+	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench cluster-split \
+		--amp-csv examples/validation/known_amps.csv \
+		--decoy-csv examples/validation/random_background.csv \
 		--out outputs/cluster_split_report.json
 
 bench-expert-ablation:
-	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench expert-ablation 
-		--amp-csv examples/validation/known_amps.csv 
-		--decoy-csv examples/validation/random_background.csv 
+	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench expert-ablation \
+		--amp-csv examples/validation/known_amps.csv \
+		--decoy-csv examples/validation/random_background.csv \
 		--out outputs/expert_ablation_report.json
 
 bench-selectivity:
-	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench selectivity 
-		--hemolysis-csv examples/validation/hemolysis_reference.csv 
+	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench selectivity \
+		--hemolysis-csv examples/validation/hemolysis_reference.csv \
 		--out outputs/selectivity_benchmark_report.json
 
 

docs/BENCHMARKING.md

@@ -15,17 +15,19 @@ Common artifacts:
 
 ## Required benchmarks
 
-| Benchmark | Purpose |
-|---|---|
-| Random baseline | Prove the pipeline is not noise |
-| Simple physicochemical baseline | Prove models beat charge/hydrophobicity alone |
-| Cluster split | Prevent near-duplicate leakage |
-| Cluster-aware CI | Honest bootstrap when positives contain near-duplicate families |
-| Time split | Test future generalization where metadata allows |
-| Hidden-positive recovery | Check whether known actives are ranked high |
-| Toxicity down-ranking | Ensure predicted risky candidates are penalized |
-| Novelty stress test | Avoid near-clones of references |
-| Within-AMP selectivity | Test whether scorers distinguish hemolytic from selective AMPs |
+| Benchmark | Purpose | Status |
+|---|---|---|
+| Random baseline | Prove the pipeline is not noise | Implemented |
+| Simple physicochemical baseline | Prove models beat charge/hydrophobicity alone | Implemented |
+| Cluster split | Prevent near-duplicate leakage | Implemented (`bench cluster-split`) |
+| Cluster-aware CI | Honest bootstrap when positives contain near-duplicate families | Implemented (cluster-aware bootstrap in `bench cluster-split`) |
+| Time split | Test future generalization where metadata allows | Deferred (metadata not available) |
+| Hidden-positive recovery | Check whether known actives are ranked high | Implemented |
+| Toxicity down-ranking | Ensure predicted risky candidates are penalized | Implemented |
+| Novelty stress test | Avoid near-clones of references | Implemented |
+| Within-AMP selectivity | Test whether scorers distinguish hemolytic from selective AMPs | Implemented (`bench selectivity`) |
+| Expert ablation | Test whether expert composite adds value over ensemble | Implemented (`bench expert-ablation`) |
+| Multi-class triage | Test selective > hemolytic > decoy ranking in one panel | Implemented (`bench triage`) |
 
 ## Minimum report fields