@helix-agent/core 0.4.0 → 0.6.0

package/dist/engine/gene-map.js

@@ -1,23 +1,5 @@
 import Database from 'better-sqlite3';
-const SCHEMA = `
-CREATE TABLE IF NOT EXISTS genes (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  failure_code TEXT NOT NULL,
-  category TEXT NOT NULL,
-  strategy TEXT NOT NULL,
-  params TEXT NOT NULL DEFAULT '{}',
-  success_count INTEGER NOT NULL DEFAULT 1,
-  avg_repair_ms REAL NOT NULL DEFAULT 0,
-  platforms TEXT NOT NULL DEFAULT '[]',
-  q_value REAL NOT NULL DEFAULT 0.5,
-  last_success_at INTEGER,
-  last_failed_at INTEGER,
-  consecutive_failures INTEGER NOT NULL DEFAULT 0,
-  created_at TEXT NOT NULL DEFAULT (datetime('now')),
-  last_used_at TEXT NOT NULL DEFAULT (datetime('now')),
-  UNIQUE(failure_code, category)
-);
-`;
+import { SEED_GENES } from './seed-genes.js';
 function parseRow(row) {
     return {
         id: row.id,
@@ -34,147 +16,279 @@ function parseRow(row) {
         lastFailedAt: row.last_failed_at,
         createdAt: row.created_at,
         lastUsedAt: row.last_used_at,
+        reasoning: row.reasoning,
+        failureAnalysis: row.failure_analysis ? JSON.parse(row.failure_analysis) : [],
+        successContext: row.success_context ? JSON.parse(row.success_context) : {},
+        failureContext: row.failure_context ? JSON.parse(row.failure_context) : {},
     };
 }
 export class GeneMap {
+    static SCHEMA_VERSION = 3;
     db;
     stmtLookup;
     stmtUpsert;
     stmtList;
     stmtCount;
     stmtUpdatePlatforms;
+    cache = new Map();
+    cacheLoadedAt = 0;
+    CACHE_TTL_MS = 30_000;
     constructor(dbPath = ':memory:') {
         this.db = new Database(dbPath);
         this.db.pragma('journal_mode = WAL');
-        this.db.exec(SCHEMA);
-        this.stmtLookup = this.db.prepare(`
-      SELECT * FROM genes WHERE failure_code = ? AND category = ? ORDER BY q_value DESC LIMIT 1
-    `);
-        this.stmtUpsert = this.db.prepare(`
-      INSERT INTO genes (failure_code, category, strategy, params, success_count, avg_repair_ms, platforms, q_value, consecutive_failures)
-      VALUES (@failureCode, @category, @strategy, @params, @successCount, @avgRepairMs, @platforms, @qValue, @consecutiveFailures)
-      ON CONFLICT(failure_code, category) DO UPDATE SET
-        strategy = @strategy,
-        params = @params,
-        success_count = success_count + 1,
-        avg_repair_ms = (avg_repair_ms * success_count + @avgRepairMs) / (success_count + 1),
-        platforms = @platforms,
-        q_value = @qValue,
-        consecutive_failures = @consecutiveFailures,
-        last_used_at = datetime('now')
-    `);
+        this.ensureSchema();
+        this.prepareStatements();
+        this.seed();
+        this.warmCache();
+    }
+    // ── Schema Versioning (D10) ──
+    ensureSchema() {
+        this.db.exec(`CREATE TABLE IF NOT EXISTS schema_version (version INTEGER NOT NULL, migrated_at DATETIME DEFAULT (datetime('now')))`);
+        const row = this.db.prepare('SELECT version FROM schema_version ORDER BY version DESC LIMIT 1').get();
+        const current = row?.version ?? 0;
+        if (current < GeneMap.SCHEMA_VERSION)
+            this.migrate(current);
+    }
+    migrate(from) {
+        const migrations = {
+            0: () => {
+                this.db.exec(`CREATE TABLE IF NOT EXISTS genes (id INTEGER PRIMARY KEY AUTOINCREMENT, failure_code TEXT NOT NULL, category TEXT NOT NULL, strategy TEXT NOT NULL, params TEXT DEFAULT '{}', success_count INTEGER DEFAULT 1, avg_repair_ms REAL DEFAULT 0, platforms TEXT DEFAULT '[]', q_value REAL DEFAULT 0.5, last_success_at INTEGER, last_failed_at INTEGER, consecutive_failures INTEGER DEFAULT 0, reasoning TEXT, failure_analysis TEXT DEFAULT '[]', success_context TEXT DEFAULT '{}', failure_context TEXT DEFAULT '{}', created_at TEXT DEFAULT (datetime('now')), last_used_at TEXT DEFAULT (datetime('now')), UNIQUE(failure_code, category))`);
+                this.db.exec(`CREATE TABLE IF NOT EXISTS repair_log (id INTEGER PRIMARY KEY AUTOINCREMENT, repair_id TEXT UNIQUE NOT NULL, failure_code TEXT NOT NULL, category TEXT NOT NULL, strategy TEXT NOT NULL, status TEXT DEFAULT 'pending', tx_hash TEXT, created_at DATETIME DEFAULT (datetime('now')), completed_at DATETIME)`);
+                this.db.exec(`CREATE TABLE IF NOT EXISTS repair_attribution (id INTEGER PRIMARY KEY AUTOINCREMENT, repair_id TEXT NOT NULL, agent_id TEXT NOT NULL, step_id TEXT, workflow TEXT, failure_code TEXT NOT NULL, category TEXT NOT NULL, strategy TEXT, success INTEGER DEFAULT 0, created_at DATETIME DEFAULT (datetime('now')))`);
+                this.db.exec('CREATE INDEX IF NOT EXISTS idx_attribution_agent ON repair_attribution(agent_id)');
+            },
+            1: () => {
+                const addCol = (t, c, type, def) => { try {
+                    this.db.exec(`ALTER TABLE ${t} ADD COLUMN ${c} ${type} DEFAULT ${def}`);
+                }
+                catch { /* exists */ } };
+                addCol('genes', 'reasoning', 'TEXT', 'NULL');
+                addCol('genes', 'failure_analysis', 'TEXT', "'[]'");
+                addCol('genes', 'success_context', 'TEXT', "'{}'");
+                addCol('genes', 'failure_context', 'TEXT', "'{}'");
+                this.db.exec(`CREATE TABLE IF NOT EXISTS repair_attribution (id INTEGER PRIMARY KEY AUTOINCREMENT, repair_id TEXT NOT NULL, agent_id TEXT NOT NULL, step_id TEXT, workflow TEXT, failure_code TEXT NOT NULL, category TEXT NOT NULL, strategy TEXT, success INTEGER DEFAULT 0, created_at DATETIME DEFAULT (datetime('now')))`);
+                this.db.exec('CREATE INDEX IF NOT EXISTS idx_attribution_agent ON repair_attribution(agent_id)');
+            },
+            2: () => {
+                this.db.exec(`CREATE TABLE IF NOT EXISTS gene_links (id INTEGER PRIMARY KEY AUTOINCREMENT, gene_a_code TEXT NOT NULL, gene_a_category TEXT NOT NULL, gene_b_code TEXT NOT NULL, gene_b_category TEXT NOT NULL, strength REAL DEFAULT 0.5, co_occurrence_count INTEGER DEFAULT 1, created_at DATETIME DEFAULT (datetime('now')), last_seen_at DATETIME DEFAULT (datetime('now')), UNIQUE(gene_a_code, gene_a_category, gene_b_code, gene_b_category))`);
+            },
+        };
+        this.db.transaction(() => {
+            for (let v = from; v < GeneMap.SCHEMA_VERSION; v++) {
+                migrations[v]?.();
+                this.db.prepare('INSERT INTO schema_version (version) VALUES (?)').run(v + 1);
+            }
+        })();
+    }
+    prepareStatements() {
+        this.stmtLookup = this.db.prepare(`SELECT * FROM genes WHERE failure_code = ? AND category = ? ORDER BY q_value DESC LIMIT 1`);
+        this.stmtUpsert = this.db.prepare(`INSERT INTO genes (failure_code, category, strategy, params, success_count, avg_repair_ms, platforms, q_value, consecutive_failures) VALUES (@failureCode, @category, @strategy, @params, @successCount, @avgRepairMs, @platforms, @qValue, @consecutiveFailures) ON CONFLICT(failure_code, category) DO UPDATE SET strategy = @strategy, params = @params, success_count = success_count + 1, avg_repair_ms = (avg_repair_ms * success_count + @avgRepairMs) / (success_count + 1), platforms = @platforms, q_value = @qValue, consecutive_failures = @consecutiveFailures, last_used_at = datetime('now')`);
         this.stmtList = this.db.prepare(`SELECT * FROM genes ORDER BY q_value DESC, success_count DESC`);
         this.stmtCount = this.db.prepare(`SELECT COUNT(*) as count FROM genes`);
-        this.stmtUpdatePlatforms = this.db.prepare(`
-      UPDATE genes SET platforms = ?, last_used_at = datetime('now') WHERE failure_code = ? AND category = ?
-    `);
+        this.stmtUpdatePlatforms = this.db.prepare(`UPDATE genes SET platforms = ?, last_used_at = datetime('now') WHERE failure_code = ? AND category = ?`);
     }
+    // ── L1 Cache ──
+    cacheKey(code, category) { return `${code}:${category}`; }
+    warmCache() { this.cache.clear(); for (const r of this.db.prepare('SELECT * FROM genes').all())
+        this.cache.set(this.cacheKey(r.failure_code, r.category), r); this.cacheLoadedAt = Date.now(); }
+    isCacheStale() { return Date.now() - this.cacheLoadedAt > this.CACHE_TTL_MS; }
+    // ── Core CRUD ──
     lookup(code, category) {
+        const key = this.cacheKey(code, category);
+        if (!this.isCacheStale() && this.cache.has(key)) {
+            const cached = this.cache.get(key);
+            this.db.prepare(`UPDATE genes SET last_used_at = datetime('now'), success_count = success_count + 1 WHERE failure_code = ? AND category = ?`).run(code, category);
+            const gene = parseRow(cached);
+            gene.successCount += 1;
+            return gene;
+        }
         const row = this.stmtLookup.get(code, category);
         if (!row)
             return null;
-        this.db.prepare(`
-      UPDATE genes SET last_used_at = datetime('now'), success_count = success_count + 1
-      WHERE failure_code = ? AND category = ?
-    `).run(code, category);
+        this.db.prepare(`UPDATE genes SET last_used_at = datetime('now'), success_count = success_count + 1 WHERE failure_code = ? AND category = ?`).run(code, category);
+        this.cache.set(key, row);
         const gene = parseRow(row);
-        gene.successCount += 1; // reflect the bump we just did
+        gene.successCount += 1;
         return gene;
     }
     addPlatform(code, category, platform) {
         const row = this.stmtLookup.get(code, category);
         if (!row)
             return;
-        const platforms = JSON.parse(row.platforms);
-        if (!platforms.includes(platform)) {
-            platforms.push(platform);
-            this.stmtUpdatePlatforms.run(JSON.stringify(platforms), code, category);
+        const p = JSON.parse(row.platforms);
+        if (!p.includes(platform)) {
+            p.push(platform);
+            this.stmtUpdatePlatforms.run(JSON.stringify(p), code, category);
+            this.cache.delete(this.cacheKey(code, category));
         }
     }
     store(gene) {
-        this.stmtUpsert.run({
-            failureCode: gene.failureCode,
-            category: gene.category,
-            strategy: gene.strategy,
-            params: JSON.stringify(gene.params, (_k, v) => typeof v === 'bigint' ? v.toString() : v),
-            successCount: gene.successCount,
-            avgRepairMs: gene.avgRepairMs,
-            platforms: JSON.stringify(gene.platforms),
-            qValue: gene.qValue ?? 0.5,
-            consecutiveFailures: gene.consecutiveFailures ?? 0,
-        });
-    }
-    /** RL update after successful repair */
+        this.stmtUpsert.run({ failureCode: gene.failureCode, category: gene.category, strategy: gene.strategy, params: JSON.stringify(gene.params, (_k, v) => typeof v === 'bigint' ? v.toString() : v), successCount: gene.successCount, avgRepairMs: gene.avgRepairMs, platforms: JSON.stringify(gene.platforms), qValue: gene.qValue ?? 0.5, consecutiveFailures: gene.consecutiveFailures ?? 0 });
+        this.cache.delete(this.cacheKey(gene.failureCode, gene.category));
+    }
     recordSuccess(code, category, repairMs) {
         const row = this.stmtLookup.get(code, category);
         if (!row)
             return;
-        const alpha = 0.1;
-        const oldQ = row.q_value;
-        const newQ = oldQ + alpha * (1.0 - oldQ);
-        this.db.prepare(`
-      UPDATE genes SET
-        q_value = ?,
-        avg_repair_ms = (avg_repair_ms * success_count + ?) / (success_count + 1),
-        success_count = success_count + 1,
-        last_success_at = ?,
-        consecutive_failures = 0,
-        last_used_at = datetime('now')
-      WHERE failure_code = ? AND category = ?
-    `).run(newQ, repairMs, Date.now(), code, category);
-    }
-    /** RL update after failed repair */
+        const newQ = row.q_value + 0.1 * (1.0 - row.q_value);
+        this.db.prepare(`UPDATE genes SET q_value = ?, avg_repair_ms = (avg_repair_ms * success_count + ?) / (success_count + 1), success_count = success_count + 1, last_success_at = ?, consecutive_failures = 0, last_used_at = datetime('now') WHERE failure_code = ? AND category = ?`).run(newQ, repairMs, Date.now(), code, category);
+        this.cache.delete(this.cacheKey(code, category));
+    }
     recordFailure(code, category) {
         const row = this.stmtLookup.get(code, category);
         if (!row)
             return;
-        const alpha = 0.1;
-        const oldQ = row.q_value;
-        const newQ = oldQ + alpha * (0.0 - oldQ);
-        this.db.prepare(`
-      UPDATE genes SET
-        q_value = ?,
-        last_failed_at = ?,
-        consecutive_failures = consecutive_failures + 1,
-        last_used_at = datetime('now')
-      WHERE failure_code = ? AND category = ?
-    `).run(newQ, Date.now(), code, category);
-    }
-    list() {
-        return this.stmtList.all().map(parseRow);
-    }
-    immuneCount() {
-        return this.stmtCount.get().count;
-    }
-    getSuccessRate(failureCode, strategy) {
-        const row = this.db.prepare(`
-      SELECT success_count, q_value FROM genes WHERE failure_code = ? AND strategy = ?
-    `).get(failureCode, strategy);
-        if (!row || row.success_count < 3)
-            return 0.5;
-        return Math.min(0.5 + (row.success_count / 100), 0.95);
-    }
-    stats() {
+        const newQ = row.q_value + 0.1 * (0.0 - row.q_value);
+        this.db.prepare(`UPDATE genes SET q_value = ?, last_failed_at = ?, consecutive_failures = consecutive_failures + 1, last_used_at = datetime('now') WHERE failure_code = ? AND category = ?`).run(newQ, Date.now(), code, category);
+        this.cache.delete(this.cacheKey(code, category));
+    }
+    list() { return this.stmtList.all().map(parseRow); }
+    immuneCount() { return this.stmtCount.get().count; }
+    getSuccessRate(failureCode, strategy) { const r = this.db.prepare(`SELECT success_count FROM genes WHERE failure_code = ? AND strategy = ?`).get(failureCode, strategy); if (!r || r.success_count < 3)
+        return 0.5; return Math.min(0.5 + (r.success_count / 100), 0.95); }
+    stats() { const rows = this.stmtList.all(); const allP = new Set(); let qSum = 0; for (const r of rows) {
+        qSum += r.q_value;
+        for (const p of JSON.parse(r.platforms))
+            allP.add(p);
+    } return { totalGenes: rows.length, avgQValue: rows.length > 0 ? Math.round((qSum / rows.length) * 100) / 100 : 0, platforms: [...allP], topStrategies: rows.slice(0, 10).map(r => ({ strategy: r.strategy, count: r.success_count })) }; }
+    // ── Seed (D9) ──
+    seed() {
+        const cnt = this.db.prepare('SELECT COUNT(*) as cnt FROM genes').get().cnt;
+        if (cnt > 0)
+            return { seeded: 0 };
+        let seeded = 0;
+        const ins = this.db.prepare(`INSERT OR IGNORE INTO genes (failure_code, category, strategy, params, success_count, avg_repair_ms, platforms, q_value, consecutive_failures) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`);
+        this.db.transaction(() => { for (const g of SEED_GENES) {
+            ins.run(g.failureCode, g.category, g.strategy, JSON.stringify(g.params), g.successCount, g.avgRepairMs, JSON.stringify(g.platforms), g.qValue, g.consecutiveFailures);
+            seeded++;
+        } })();
+        return { seeded };
+    }
+    // ── Gene Combine (OPT-3) ──
+    combine() {
+        let merged = 0;
+        const groups = this.db.prepare(`SELECT failure_code, category, COUNT(*) as cnt FROM genes GROUP BY failure_code, category HAVING cnt > 1`).all();
+        for (const g of groups) {
+            const genes = this.db.prepare(`SELECT * FROM genes WHERE failure_code = ? AND category = ? ORDER BY q_value DESC`).all(g.failure_code, g.category);
+            if (genes.length <= 1)
+                continue;
+            const best = genes[0];
+            const allP = new Set();
+            let totalSC = 0;
+            let wMs = 0;
+            for (const gn of genes) {
+                totalSC += gn.success_count;
+                wMs += gn.avg_repair_ms * gn.success_count;
+                for (const p of JSON.parse(gn.platforms))
+                    allP.add(p);
+            }
+            const maxQ = Math.max(...genes.map(gn => gn.q_value));
+            this.db.prepare(`UPDATE genes SET platforms = ?, success_count = ?, avg_repair_ms = ?, q_value = ?, last_used_at = datetime('now') WHERE id = ?`).run(JSON.stringify([...allP]), totalSC, wMs / Math.max(totalSC, 1), maxQ, best.id);
+            for (const gn of genes.slice(1)) {
+                this.db.prepare('DELETE FROM genes WHERE id = ?').run(gn.id);
+                merged++;
+            }
+        }
+        if (merged > 0)
+            this.warmCache();
+        return { merged };
+    }
+    gc() {
+        const { merged } = this.combine();
+        const pruned = this.db.prepare(`DELETE FROM genes WHERE q_value < 0.1 AND consecutive_failures >= 3`).run().changes;
+        const archived = this.db.prepare(`SELECT COUNT(*) as cnt FROM genes WHERE last_used_at < datetime('now', '-180 days')`).get().cnt;
+        if (pruned > 0)
+            this.warmCache();
+        return { merged, pruned, archived };
+    }
+    // ── Reasoning (OPT-4) ──
+    recordFailureAnalysis(code, category, analysis) {
+        const row = this.stmtLookup.get(code, category);
+        if (!row)
+            return;
+        const existing = row.failure_analysis ? JSON.parse(row.failure_analysis) : [];
+        const updated = [...existing, `[${new Date().toISOString().slice(0, 10)}] ${analysis}`].slice(-5);
+        this.db.prepare(`UPDATE genes SET failure_analysis = ? WHERE failure_code = ? AND category = ?`).run(JSON.stringify(updated), code, category);
+        this.cache.delete(this.cacheKey(code, category));
+    }
+    updateContext(code, category, success, context) {
+        const row = this.stmtLookup.get(code, category);
+        if (!row)
+            return;
+        if (success) {
+            const ctx = row.success_context ? JSON.parse(row.success_context) : {};
+            if (context.chain && !(ctx.chains ?? []).includes(context.chain))
+                ctx.chains = [...(ctx.chains ?? []), context.chain];
+            if (context.platform && !(ctx.platforms ?? []).includes(context.platform))
+                ctx.platforms = [...(ctx.platforms ?? []), context.platform];
+            this.db.prepare('UPDATE genes SET success_context = ? WHERE failure_code = ? AND category = ?').run(JSON.stringify(ctx), code, category);
+        }
+        else {
+            const ctx = row.failure_context ? JSON.parse(row.failure_context) : {};
+            if (context.chain && !(ctx.chains ?? []).includes(context.chain))
+                ctx.chains = [...(ctx.chains ?? []), context.chain];
+            this.db.prepare('UPDATE genes SET failure_context = ? WHERE failure_code = ? AND category = ?').run(JSON.stringify(ctx), code, category);
+        }
+        this.cache.delete(this.cacheKey(code, category));
+    }
+    // ── Idempotency (D5) ──
+    generateRepairId() { return `repair_${Date.now()}_${Math.random().toString(36).slice(2, 8)}`; }
+    checkRepairInProgress(code, category) {
+        const r = this.db.prepare(`SELECT repair_id, status, tx_hash FROM repair_log WHERE failure_code = ? AND category = ? AND status IN ('pending','completed') AND created_at > datetime('now','-5 minutes') ORDER BY created_at DESC LIMIT 1`).get(code, category);
+        if (!r)
+            return { inProgress: false };
+        if (r.status === 'pending')
+            return { inProgress: true, repairId: r.repair_id };
+        if (r.status === 'completed' && r.tx_hash)
+            return { inProgress: true, repairId: r.repair_id, txHash: r.tx_hash };
+        return { inProgress: false };
+    }
+    logRepairStart(id, code, category, strategy) { this.db.prepare(`INSERT OR IGNORE INTO repair_log (repair_id, failure_code, category, strategy, status) VALUES (?,?,?,?,'pending')`).run(id, code, category, strategy); }
+    logRepairComplete(id, txHash) { this.db.prepare(`UPDATE repair_log SET status='completed', tx_hash=?, completed_at=datetime('now') WHERE repair_id=?`).run(txHash ?? null, id); }
+    logRepairFailed(id) { this.db.prepare(`UPDATE repair_log SET status='failed', completed_at=datetime('now') WHERE repair_id=?`).run(id); }
+    // ── Attribution (OPT-10) ──
+    recordAttribution(data) {
+        this.db.prepare(`INSERT INTO repair_attribution (repair_id, agent_id, step_id, workflow, failure_code, category, strategy, success) VALUES (?,?,?,?,?,?,?,?)`).run(data.repairId, data.agentId, data.stepId ?? null, data.workflow ?? null, data.failureCode, data.category, data.strategy ?? null, data.success ? 1 : 0);
+    }
+    getAgentStats(agentId) {
+        const total = this.db.prepare('SELECT COUNT(*) as cnt FROM repair_attribution WHERE agent_id = ?').get(agentId).cnt;
+        const cats = this.db.prepare(`SELECT category, COUNT(*) as cnt FROM repair_attribution WHERE agent_id = ? GROUP BY category ORDER BY cnt DESC LIMIT 5`).all(agentId);
+        const steps = this.db.prepare(`SELECT step_id, COUNT(*) as cnt FROM repair_attribution WHERE agent_id = ? AND step_id IS NOT NULL GROUP BY step_id ORDER BY cnt DESC LIMIT 5`).all(agentId);
+        const ok = this.db.prepare('SELECT COUNT(*) as cnt FROM repair_attribution WHERE agent_id = ? AND success = 1').get(agentId).cnt;
+        return { totalFailures: total, topCategories: cats.map(c => ({ category: c.category, count: c.cnt })), topSteps: steps.map(s => ({ stepId: s.step_id, count: s.cnt })), successRate: total > 0 ? ok / total : 0 };
+    }
+    getGlobalAttributionStats() {
+        const total = this.db.prepare('SELECT COUNT(*) as cnt FROM repair_attribution').get().cnt;
+        const agents = this.db.prepare(`SELECT agent_id, COUNT(*) as cnt FROM repair_attribution GROUP BY agent_id ORDER BY cnt DESC LIMIT 10`).all();
+        const cats = this.db.prepare(`SELECT category, COUNT(*) as cnt FROM repair_attribution GROUP BY category ORDER BY cnt DESC LIMIT 10`).all();
+        const ok = this.db.prepare('SELECT COUNT(*) as cnt FROM repair_attribution WHERE success = 1').get().cnt;
+        return { totalRepairs: total, topAgents: agents.map(a => ({ agentId: a.agent_id, failures: a.cnt })), topCategories: cats.map(c => ({ category: c.category, count: c.cnt })), overallSuccessRate: total > 0 ? ok / total : 0 };
+    }
+    // ── Gene Links (OPT-5: A-Mem paper) ──
+    recordCoOccurrence(codeA, catA, codeB, catB) {
+        const [a, b] = [{ code: codeA, cat: catA }, { code: codeB, cat: catB }].sort((x, y) => `${x.code}:${x.cat}`.localeCompare(`${y.code}:${y.cat}`));
+        this.db.prepare(`INSERT INTO gene_links (gene_a_code, gene_a_category, gene_b_code, gene_b_category) VALUES (?,?,?,?) ON CONFLICT(gene_a_code, gene_a_category, gene_b_code, gene_b_category) DO UPDATE SET co_occurrence_count = co_occurrence_count + 1, strength = MIN(1.0, strength + 0.1), last_seen_at = datetime('now')`).run(a.code, a.cat, b.code, b.cat);
+    }
+    getRelatedFailures(code, category) {
+        return this.db.prepare(`SELECT CASE WHEN gene_a_code = ? AND gene_a_category = ? THEN gene_b_code ELSE gene_a_code END as rc, CASE WHEN gene_a_code = ? AND gene_a_category = ? THEN gene_b_category ELSE gene_a_category END as rcat, strength, co_occurrence_count as co FROM gene_links WHERE (gene_a_code = ? AND gene_a_category = ?) OR (gene_b_code = ? AND gene_b_category = ?) ORDER BY strength DESC LIMIT 5`).all(code, category, code, category, code, category, code, category).map(r => ({ code: r.rc, category: r.rcat, strength: r.strength, coOccurrences: r.co }));
+    }
+    // ── Health (for CLI) ──
+    health() {
         const rows = this.stmtList.all();
-        const allPlatforms = new Set();
+        const allP = new Set();
         let qSum = 0;
         for (const r of rows) {
             qSum += r.q_value;
             for (const p of JSON.parse(r.platforms))
-                allPlatforms.add(p);
+                allP.add(p);
         }
         return {
             totalGenes: rows.length,
-            avgQValue: rows.length > 0 ? Math.round((qSum / rows.length) * 100) / 100 : 0,
-            platforms: [...allPlatforms],
-            topStrategies: rows.slice(0, 10).map(r => ({
-                strategy: r.strategy,
-                count: r.success_count,
-            })),
+            avgQValue: rows.length > 0 ? qSum / rows.length : 0,
+            platforms: [...allP],
+            topStrategies: rows.slice(0, 10).map(r => ({ strategy: r.strategy, qValue: r.q_value, count: r.success_count })),
         };
     }
-    close() {
-        this.db.close();
-    }
+    close() { this.db.close(); }
 }
 //# sourceMappingURL=gene-map.js.map

package/dist/engine/gene-map.js.map

@@ -1 +1 @@
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package/dist/engine/pcec.d.ts

@@ -13,8 +13,10 @@ export declare class PcecEngine {
     };
     private readonly MAX_CYCLES;
     private cycleCount;
-    /** D6: Systematic failure tracker — detect repeated identical failures */
+    /** D6: Systematic failure tracker */
     private failureTracker;
+    /** OPT-5: Recent failures for co-occurrence detection */
+    private recentFailures;
     constructor(geneMap: GeneMap, agentId?: string, options?: WrapOptions);
     private checkSystematic;
     registerAdapter(adapter: PlatformAdapter): void;

package/dist/engine/pcec.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pcec.d.ts","sourceRoot":"","sources":["../../src/engine/pcec.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAIxC,OAAO,KAAK,EAEV,WAAW,EAEX,eAAe,EAEf,YAAY,EACZ,WAAW,EACZ,MAAM,YAAY,CAAC;AA6BpB,qBAAa,UAAU;IACrB,OAAO,CAAC,QAAQ,CAAyB;IACzC,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,QAAQ,CAAgB;IAChC,OAAO,CAAC,OAAO,CAAc;IACtB,KAAK;;;;MAAkD;IAC9D,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAM;IACjC,OAAO,CAAC,UAAU,CAAK;IACvB,0EAA0E;IAC1E,OAAO,CAAC,cAAc,CAAkF;gBAE5F,OAAO,EAAE,OAAO,EAAE,OAAO,GAAE,MAAkB,EAAE,OAAO,CAAC,EAAE,WAAW;IAOhF,OAAO,CAAC,eAAe;IAiBvB,eAAe,CAAC,OAAO,EAAE,eAAe,GAAG,IAAI;IAI/C,kFAAkF;IAClF,OAAO,CAAC,kBAAkB;IAS1B,OAAO,CAAC,QAAQ;IAkBhB,OAAO,CAAC,mBAAmB;YAWb,MAAM;IAyBd,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,OAAO,CAAC,YAAY,CAAC;IAuOpF,QAAQ;;;;;;;IAQR,UAAU,IAAI,OAAO;CAGtB"}
+{"version":3,"file":"pcec.d.ts","sourceRoot":"","sources":["../../src/engine/pcec.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAIxC,OAAO,KAAK,EAEV,WAAW,EAEX,eAAe,EAEf,YAAY,EACZ,WAAW,EACZ,MAAM,YAAY,CAAC;AA8BpB,qBAAa,UAAU;IACrB,OAAO,CAAC,QAAQ,CAAyB;IACzC,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,QAAQ,CAAgB;IAChC,OAAO,CAAC,OAAO,CAAc;IACtB,KAAK;;;;MAAkD;IAC9D,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAM;IACjC,OAAO,CAAC,UAAU,CAAK;IACvB,qCAAqC;IACrC,OAAO,CAAC,cAAc,CAAkF;IACxG,yDAAyD;IACzD,OAAO,CAAC,cAAc,CAA+D;gBAEzE,OAAO,EAAE,OAAO,EAAE,OAAO,GAAE,MAAkB,EAAE,OAAO,CAAC,EAAE,WAAW;IAOhF,OAAO,CAAC,eAAe;IAiBvB,eAAe,CAAC,OAAO,EAAE,eAAe,GAAG,IAAI;IAI/C,kFAAkF;IAClF,OAAO,CAAC,kBAAkB;IAS1B,OAAO,CAAC,QAAQ;IAsBhB,OAAO,CAAC,mBAAmB;YAWb,MAAM;IAyBd,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,OAAO,CAAC,YAAY,CAAC;IAiRpF,QAAQ;;;;;;;IAQR,UAAU,IAAI,OAAO;CAGtB"}

package/dist/engine/pcec.js

@@ -2,6 +2,7 @@ import { bus } from './bus.js';
 import { evaluate } from './evaluate.js';
 import { HelixProvider } from './provider.js';
 import { REVENUE_AT_RISK } from './types.js';
+import { getRootCause } from './root-causes.js';
 // Category C strategies that move funds — require 'full' mode
 const FUND_MOVEMENT_STRATEGIES = [
     'swap_currency', 'split_transaction', 'topup_from_reserve',
@@ -35,8 +36,10 @@ export class PcecEngine {
     stats = { repairs: 0, savedRevenue: 0, immuneHits: 0 };
     MAX_CYCLES = 50;
     cycleCount = 0;
-    /** D6: Systematic failure tracker — detect repeated identical failures */
+    /** D6: Systematic failure tracker */
     failureTracker = new Map();
+    /** OPT-5: Recent failures for co-occurrence detection */
+    recentFailures = [];
     constructor(geneMap, agentId = 'default', options) {
         this.geneMap = geneMap;
         this.agentId = agentId;
@@ -81,8 +84,12 @@ export class PcecEngine {
         }
         for (const adapter of this.adapters) {
             const result = adapter.perceive(error, context);
-            if (result)
+            if (result) {
+                const rc = getRootCause(result.code, result.category);
+                if (rc)
+                    result.rootCauseHint = rc.hint;
                 return result;
+            }
         }
         return {
             code: 'unknown', category: 'unknown', severity: 'medium',
@@ -141,6 +148,15 @@ export class PcecEngine {
             bus.emit('error', this.agentId, { reason: 'SYSTEMATIC', message: systematicWarning });
             this.options.onSystematic?.(systematicWarning, failure);
         }
+        // ── OPT-5: Co-occurrence tracking for Gene Links ──
+        const now = Date.now();
+        this.recentFailures = this.recentFailures.filter(f => now - f.timestamp < 60_000);
+        for (const recent of this.recentFailures) {
+            if (recent.code !== failure.code || recent.category !== failure.category) {
+                this.geneMap.recordCoOccurrence(recent.code, recent.category, failure.code, failure.category);
+            }
+        }
+        this.recentFailures.push({ code: failure.code, category: failure.category, timestamp: now });
         // ── GENE MAP LOOKUP (with Q-value ranking) ──
         const existingGene = this.geneMap.lookup(failure.code, failure.category);
         if (existingGene && existingGene.qValue > 0.3) {
@@ -240,9 +256,13 @@ export class PcecEngine {
             winner: winner.strategy, score: winner.score, platform: winner.platform,
             allScores: scored.map(c => ({ strategy: c.strategy, score: c.score })),
         });
-        // ── BUILD EXPLANATION ──
+        // ── BUILD EXPLANATION (with root cause hints OPT-7) ──
+        const rootCause = getRootCause(failure.code, failure.category);
         const explanation = [
             `Perceived: ${failure.code} → ${failure.category} [${failure.severity}] (${failure.platform})`,
+            rootCause ? `Root cause: ${rootCause.likelyCause}` : '',
+            rootCause ? `Suggested: ${rootCause.suggestedAction}` : '',
+            rootCause?.isLikelySystematic ? '⚠️ Likely systematic — check configuration.' : '',
             `Candidates: ${scored.map(c => `${c.strategy}(${c.score})`).join(', ')}`,
             `Selected: ${winner.strategy} (score: ${winner.score})`,
             skippedStrategies.length > 0 ? `Skipped: ${skippedStrategies.join(', ')}` : '',
@@ -263,7 +283,19 @@ export class PcecEngine {
                 costEstimate: winner.estimatedCostUsd, skippedStrategies,
             });
         }
+        // ── IDEMPOTENCY CHECK (D5) ──
+        const inProgress = this.geneMap.checkRepairInProgress(failure.code, failure.category);
+        if (inProgress.inProgress) {
+            return makeResult({
+                success: !!inProgress.txHash, mode, failure, candidates: scored, winner,
+                explanation: explanation + `\nIdempotency: repair already ${inProgress.txHash ? 'completed' : 'in progress'} (${inProgress.repairId})`,
+                verified: !!inProgress.txHash,
+                costEstimate: winner.estimatedCostUsd, skippedStrategies,
+            });
+        }
         // ── COMMIT ──
+        const repairId = this.geneMap.generateRepairId();
+        this.geneMap.logRepairStart(repairId, failure.code, failure.category, winner.strategy);
         const commitResult = await this.provider.execute(winner.strategy, failure, context);
         const totalMs = Date.now() - start;
         const revenue = REVENUE_AT_RISK[failure.category] ?? 50;
@@ -278,6 +310,8 @@ export class PcecEngine {
             this.stats.repairs++;
             this.stats.savedRevenue += revenue;
             this.cycleCount = 0;
+            const txHash = commitResult.overrides.txHash;
+            this.geneMap.logRepairComplete(repairId, txHash);
             const gene = {
                 failureCode: failure.code, category: failure.category,
                 strategy: winner.strategy, params: commitResult.overrides,
@@ -295,6 +329,10 @@ export class PcecEngine {
                 totalRepairs: this.stats.repairs, savedRevenue: this.stats.savedRevenue,
                 immuneHits: this.stats.immuneHits, geneCount: this.geneMap.immuneCount(),
             });
+            // OPT-4: Update context + OPT-10: Attribution
+            this.geneMap.updateContext(failure.code, failure.category, true, { chain: context?.chainId?.toString(), platform: failure.platform });
+            this.geneMap.recordAttribution({ repairId, agentId: this.agentId, stepId: context?.stepId, workflow: context?.workflow, failureCode: failure.code, category: failure.category, strategy: winner.strategy, success: true });
+            const attribution = { agentId: this.agentId, stepId: context?.stepId, workflow: context?.workflow, timestamp: Date.now() };
             return makeResult({
                 success: true, mode, verified: true,
                 explanation: explanation + '\n✓ Verified',
@@ -302,9 +340,14 @@ export class PcecEngine {
                 gene: this.geneMap.lookup(failure.code, failure.category) ?? gene,
                 totalMs, revenueProtected: revenue,
                 costEstimate: winner.estimatedCostUsd, skippedStrategies,
+                attribution,
             });
         }
         // Verify failed
+        this.geneMap.logRepairFailed(repairId);
+        this.geneMap.updateContext(failure.code, failure.category, false, { chain: context?.chainId?.toString(), platform: failure.platform });
+        this.geneMap.recordFailureAnalysis(failure.code, failure.category, `Strategy '${winner.strategy}' failed: ${commitResult.description}`);
+        this.geneMap.recordAttribution({ repairId, agentId: this.agentId, stepId: context?.stepId, workflow: context?.workflow, failureCode: failure.code, category: failure.category, strategy: winner.strategy, success: false });
         if (existingGene) {
             this.geneMap.recordFailure(failure.code, failure.category);
         }
@@ -312,6 +355,7 @@ export class PcecEngine {
             failure, mode, candidates: scored, winner, totalMs,
             explanation: explanation + '\n✗ Verification failed',
             costEstimate: winner.estimatedCostUsd, skippedStrategies,
+            attribution: { agentId: this.agentId, stepId: context?.stepId, workflow: context?.workflow, timestamp: Date.now() },
         });
     }
     getStats() {