Review gate REJECT attempt 1/10: The diff deletes scidex/agora/verify_claims.py (570 lines) and 4 spec files that were just merged in PRs #1234, #1259, and #1260 — these deletions are unrelated to the task (which is a database-only counter-evidence backfill) and would revert recently landed work. The branch appears to be based on a stale commit predating those merges.
Add real counter-evidence review to active hypotheses whose evidence_against field is empty. This keeps confidence scores, debates, and markets from becoming one-sided summaries of support only.
evidence_against entries or documented no-counterevidence rationaleevidence_against counts are recordedevidence_against, prioritizing high-confidence or market-relevant rows.c488a683-47f - Agora questacquire_fail:worktree_creation_failed:branch_held_by_other:held_by=/tmp/task-2f7e1600-w5 — a stale worktree directory from a prior agent holding the branch lock./tmp/task-2f7e1600-w5 directory.evidence_against count from 143 to 123 across prior batches, but the live PostgreSQL count remains 123, so the task is still relevant.Test hypothesis 0 rows and curate the next 10 highest-scoring real non-archived hypotheses with empty evidence_against.hyp-lyso-snca-cf55ff77a38a (VPS35/GBA1 retromer-GCase), hyp-lyso-snca-f7d4ff9f589e (SNCA/ESCRT), 9f06a8cc-c784-4260-81f8-cd582c14b706 (APOE4 lipid droplet microglia), 44b404ab-eabb-45a2-ab3a-9e2f3ecf3b7b (CCL2-CCR2/MMP9 ALS NMJ), h-metrep-e58337c5a061 (dasatinib+quercetin senolytics), h-metrep-e5842c76ad1d (NG2+ OPC metabolic checkpoint), h-metrep-033391a02408 (NMN/SLC12A8/SIRT1), h-metrep-5d3e6f6af6cd (DRP1/MFN2 mitochondrial dynamics), 897f3e4a-f96a-4a65-b3c8-61e20a1054da (FUS arginine methylation), and 29a49684-e9d9-48f5-9731-3904b839654b (KDM6A female-biased microglia).evidence_against JSON arrays, evidence_validation_score values of 0.40-0.50, and refreshed last_evidence_update / last_mutated_at.alternative_mechanism (4), contradictory_mechanism (6), incomplete_evidence (4), mixed_result (2), methodological_caution (2), null_result (1). Strengths: strong (2), moderate (16), weak (1).evidence_against; after count is 113. A sample query confirmed every target row now has 1-2 evidence items with PMID or DOI provenance and a non-null evidence validation score.quest_engine.py.status='active' query returned 0 rows because current hypothesis statuses are proposed, promoted, debated, and archived; the quest predicate uses COALESCE(status, '') <> 'archived'.evidence_against; all 10 were duplicate proposed Test: TREM2 enhances amyloid clearance rows.scidex.core.database.get_db(), using PubMed-backed citations and explicit search provenance.hyp_test_f358dd4b, hyp_test_656bc496, hyp_test_d2990401, hyp_test_c4cd97c6, hyp_test_c201b8c0, hyp_test_852af3c6, hyp_test_490ced0b, hyp_test_0215075b, hyp_test_2750d4e9, hyp_test_f15ab6d9.evidence_against; verification query reported 722/722 non-archived hypotheses with non-empty evidence-against arrays.scidex status shows PostgreSQL reachable, API/nginx/linkcheck/Neo4j active; agent and bridge were activating, forge-improve inactive.{
"requirements": {
"analysis": 7,
"reasoning": 6
},
"max_iterations": 15,
"_watchdog_repair_task_id": "239198f4-f1f5-44a0-a330-fea7d4723538",
"_watchdog_repair_created_at": "2026-04-28T22:32:43.960164+00:00",
"_gate_retry_count": 1,
"_gate_last_decision": "REJECT",
"_gate_last_reason": "The diff deletes scidex/agora/verify_claims.py (570 lines) and 4 spec files that were just merged in PRs #1234, #1259, and #1260 \u2014 these deletions are unrelated to the task (which is a database-only counter-evidence backfill) and would revert recently landed work. The branch appears to be based on a stale commit predating those merges.",
"_gate_judge_used": "max_outlook1:claude-auto",
"_gate_last_instructions": "Rebase the working branch onto current main (HEAD = 7270817e2) so the recent merges of verify_claims.py and the Cycle 3 spec files are preserved.\nReduce the commit to only the intended additions: the new spec file docs/planning/specs/quest_engine_hypothesis_negative_evidence_backfill_spec.md (and any work-log edits to existing specs you actually intended).\nDo NOT delete scidex/agora/verify_claims.py, agora_hypothesis_validation_gate_spec.md, exchange_experiment_to_market_bridge_spec.md, forge_benchmark_evaluation_harness_spec.md, or codex_ambitious_quest_task_generator_spec.md \u2014 those were added by other tasks and remain active.\nVerify the actual DB-side counter-evidence updates listed in the work log are persisted in PostgreSQL (the task's real deliverable lives in the DB, not in this diff).",
"_gate_branch": "orchestra/task/2f7e1600-add-counter-evidence-reviews-to-10-hypot",
"_gate_changed_files": [
"docs/planning/specs/6abdeecf_pubmed_evidence_20_hypotheses_spec.md",
"docs/planning/specs/agora_hypothesis_validation_gate_spec.md",
"docs/planning/specs/agora_mechanistic_claim_verifier_spec.md",
"docs/planning/specs/codex_ambitious_quest_task_generator_spec.md",
"docs/planning/specs/exchange_experiment_to_market_bridge_spec.md",
"docs/planning/specs/forge_benchmark_evaluation_harness_spec.md",
"docs/planning/specs/quest_engine_hypothesis_negative_evidence_backfill_spec.md",
"scidex/agora/verify_claims.py"
],
"_gate_diff_stat": ".../6abdeecf_pubmed_evidence_20_hypotheses_spec.md | 8 -\n .../specs/agora_hypothesis_validation_gate_spec.md | 62 ---\n .../specs/agora_mechanistic_claim_verifier_spec.md | 33 --\n .../codex_ambitious_quest_task_generator_spec.md | 78 ---\n .../exchange_experiment_to_market_bridge_spec.md | 91 ----\n .../forge_benchmark_evaluation_harness_spec.md | 70 ---\n ...e_hypothesis_negative_evidence_backfill_spec.md | 42 ++\n scidex/agora/verify_claims.py | 570 ---------------------\n 8 files changed, 42 insertions(+), 912 deletions(-)",
"_gate_history": [
{
"ts": "2026-04-28 22:50:40",
"decision": "REJECT",
"reason": "The diff deletes scidex/agora/verify_claims.py (570 lines) and 4 spec files that were just merged in PRs #1234, #1259, and #1260 \u2014 these deletions are unrelated to the task (which is a database-only counter-evidence backfill) and would revert recently landed work. The branch appears to be based on a stale commit predating those merges.",
"instructions": "Rebase the working branch onto current main (HEAD = 7270817e2) so the recent merges of verify_claims.py and the Cycle 3 spec files are preserved.\nReduce the commit to only the intended additions: the new spec file docs/planning/specs/quest_engine_hypothesis_negative_evidence_backfill_spec.md (and any work-log edits to existing specs you actually intended).\nDo NOT delete scidex/agora/verify_claims.py, agora_hypothesis_validation_gate_spec.md, exchange_experiment_to_market_bridge_spec.md, forge_benchmark_evaluation_harness_spec.md, or codex_ambitious_quest_task_generator_spec.md \u2014 those were added by other tasks and remain active.\nVerify the actual DB-side counter-evidence updates listed in the work log are persisted in PostgreSQL (the task's real deliverable lives in the DB, not in this dif",
"judge_used": "max_outlook1:claude-auto",
"actor": "minimax:33",
"retry_count": 1
}
]
}