progmune-runtime 2.1.6 → 3.2.0

package/dist/protocol-foundation.js

@@ -0,0 +1,322 @@
+"use strict";
+/**
+ * P6.0: Protocol Foundation Model
+ *
+ * Scales protocol extraction from manual rules to automatic,
+ * code-driven discovery. The Protocol VM's knowledge base
+ * grows organically from real code patterns.
+ *
+ * Target: Discovery Rate 43% → 70%+
+ *
+ * Improvements over basic Protocol Extractor (P5.5):
+ *   1. Intelligent state naming (FILE_OPEN, not STATE_OPEN)
+ *   2. Domain-specific clustering (group related functions)
+ *   3. Confidence-weighted rule merging
+ *   4. Direct integration with benchmark evaluation
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.inferStateName = inferStateName;
+exports.inferEnhancedRules = inferEnhancedRules;
+exports.extractProtocolFoundation = extractProtocolFoundation;
+exports.enhancedRulesToMap = enhancedRulesToMap;
+exports.measureDiscoveryImpact = measureDiscoveryImpact;
+exports.printFoundationReport = printFoundationReport;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const protocol_extractor_1 = require("./protocol-extractor");
+const repo_evaluator_1 = require("./repo-evaluator");
+const protocol_coverage_1 = require("./protocol-coverage");
+const evaluation_campaign_1 = require("./evaluation-campaign");
+const discovery_analytics_1 = require("./discovery-analytics");
+// ═══════════════════════════════════════════════════════════════
+// Intelligent State Naming
+// ═══════════════════════════════════════════════════════════════
+const DOMAIN_KEYWORDS = {
+    FILE: ["file", "fopen", "fread", "fwrite", "fclose", "open", "read", "write", "close", "flush", "sync", "stat"],
+    DB: ["db", "connect", "query", "insert", "update", "delete", "disconnect", "sql", "transaction", "commit", "rollback"],
+    AUTH: ["auth", "login", "logout", "password", "token", "jwt", "session", "verify", "credential", "authenticate"],
+    NET: ["socket", "connect", "bind", "listen", "accept", "send", "recv", "http", "request", "response"],
+    MEM: ["alloc", "malloc", "free", "realloc", "mem", "memory", "buffer", "release"],
+    PROC: ["fork", "exec", "wait", "kill", "signal", "process", "thread", "mutex", "lock", "unlock"],
+};
+const STATE_SUFFIXES = {
+    open: "_OPEN", close: "_CLOSED", connect: "_CONNECTED", disconnect: "_CLOSED",
+    create: "_CREATED", destroy: "_DESTROYED", init: "_INITIALIZED", alloc: "_ALLOCATED",
+    free: "_FREED", lock: "_LOCKED", unlock: "_UNLOCKED", start: "_STARTED",
+    stop: "_STOPPED", begin: "_ACTIVE", end: "_COMPLETED", login: "_AUTHENTICATED",
+    logout: "_UNAUTHENTICATED", read: "_READY", write: "_DIRTY",
+    verify: "_VERIFIED", generate: "_ISSUED", send: "_SENT", recv: "_RECEIVED",
+};
+/** Infer a meaningful state name from a function name and its role. */
+function inferStateName(fn, role) {
+    const lower = fn.toLowerCase();
+    // Find domain
+    let domain = "STATE";
+    for (const [dom, keywords] of Object.entries(DOMAIN_KEYWORDS)) {
+        if (keywords.some(kw => lower.includes(kw))) {
+            domain = dom;
+            break;
+        }
+    }
+    // Find state suffix
+    let suffix = "";
+    for (const [key, val] of Object.entries(STATE_SUFFIXES)) {
+        if (lower.includes(key)) {
+            suffix = val;
+            break;
+        }
+    }
+    // Default suffixes by role
+    if (!suffix) {
+        suffix = role === "pre" ? "_REQUIRED" : role === "invalidate" ? "_INVALIDATED" : "_PRODUCED";
+    }
+    return `${domain}${suffix}`;
+}
+/**
+ * Enhanced protocol rule inference with intelligent state names.
+ */
+function inferEnhancedRules(pairs, minFrequency = 3) {
+    // Count transition frequencies
+    const transitions = new Map();
+    const fnFreq = new Map();
+    for (const p of pairs) {
+        const key = `${p.from}→${p.to}`;
+        transitions.set(key, (transitions.get(key) || 0) + 1);
+        fnFreq.set(p.from, (fnFreq.get(p.from) || 0) + 1);
+        fnFreq.set(p.to, (fnFreq.get(p.to) || 0) + 1);
+    }
+    const maxFreq = Math.max(1, ...[...transitions.values()]);
+    const rules = [];
+    // Build per-function state maps
+    const fnStates = new Map();
+    for (const [key, freq] of transitions) {
+        if (freq < minFrequency)
+            continue;
+        const [fnA, fnB] = key.split("→");
+        const confidence = freq / maxFreq;
+        // Infer state name from the PRODUCER (fnA), not consumer
+        const stateName = inferStateName(fnA, "post");
+        // fnA produces it, fnB requires it
+        // Track for fnA
+        const aStates = fnStates.get(fnA) || { produced: new Set(), required: new Set(), invalidated: new Set() };
+        aStates.produced.add(stateName);
+        fnStates.set(fnA, aStates);
+        // Track for fnB
+        const bStates = fnStates.get(fnB) || { produced: new Set(), required: new Set(), invalidated: new Set() };
+        bStates.required.add(stateName);
+        fnStates.set(fnB, bStates);
+    }
+    // Second pass: detect invalidation patterns
+    for (const [key, freq] of transitions) {
+        if (freq < minFrequency)
+            continue;
+        const [fnA, fnB] = key.split("→");
+        // Check if fnB is a "closer" that invalidates fnA's produced state
+        const aStates = fnStates.get(fnA);
+        const bStates = fnStates.get(fnB);
+        if (!aStates || !bStates)
+            continue;
+        const isCloser = ["close", "disconnect", "logout", "free", "destroy", "release", "stop", "end", "finish"]
+            .some(kw => fnB.includes(kw));
+        const isOpener = ["open", "connect", "login", "create", "alloc", "init", "start", "begin"]
+            .some(kw => fnA.includes(kw));
+        if (isCloser && isOpener) {
+            // fnB invalidates what fnA produced
+            for (const state of aStates.produced) {
+                bStates.invalidated.add(state);
+            }
+        }
+    }
+    // Convert to rules
+    const maxFnFreq = Math.max(1, ...[...fnFreq.values()]);
+    for (const [fn, states] of fnStates) {
+        const freq = fnFreq.get(fn) || 1;
+        const confidence = Math.min(1, freq / maxFnFreq);
+        const domain = inferDomain(fn);
+        rules.push({
+            function: fn,
+            pre_states: [...states.required],
+            post_states: [...states.produced],
+            invalidate: states.invalidated.size > 0 ? [...states.invalidated] : undefined,
+            confidence,
+            evidence: freq,
+            domain,
+            stateNames: {
+                pre: [...states.required],
+                post: [...states.produced],
+                invalidate: [...states.invalidated],
+            },
+        });
+    }
+    return rules.sort((a, b) => b.confidence - a.confidence);
+}
+function inferDomain(fn) {
+    const lower = fn.toLowerCase();
+    for (const [dom, keywords] of Object.entries(DOMAIN_KEYWORDS)) {
+        if (keywords.some(kw => lower.includes(kw)))
+            return dom;
+    }
+    return "GENERAL";
+}
+/**
+ * Extract a protocol foundation from a repository.
+ *
+ * Uses enhanced rule inference with intelligent state naming
+ * and frequency-based confidence scoring.
+ */
+function extractProtocolFoundation(repoPath, protocolName, maxFiles = 200, minFrequency = 3) {
+    const files = (0, repo_evaluator_1.scanRepository)(repoPath, maxFiles);
+    const allPairs = [];
+    for (const fp of files) {
+        try {
+            const code = fs.readFileSync(fp, "utf-8");
+            allPairs.push(...(0, protocol_extractor_1.extractCallPairs)(code, fp));
+        }
+        catch { /* skip */ }
+    }
+    const rules = inferEnhancedRules(allPairs, minFrequency);
+    const states = new Set();
+    for (const r of rules) {
+        for (const s of r.pre_states)
+            states.add(s);
+        for (const s of r.post_states)
+            states.add(s);
+        if (r.invalidate)
+            for (const s of r.invalidate)
+                states.add(s);
+    }
+    // Compare against hand-written baseline
+    const defs = (0, protocol_coverage_1.loadDefaultProtocolDefinitions)();
+    const handWrittenFns = new Set();
+    for (const p of defs)
+        for (const fn of p.rules.keys())
+            handWrittenFns.add(fn);
+    const extractedFns = new Set(rules.map(r => r.function));
+    let overlap = 0;
+    for (const fn of extractedFns) {
+        if (handWrittenFns.has(fn))
+            overlap++;
+    }
+    const avgConf = rules.length > 0 ? rules.reduce((s, r) => s + r.confidence, 0) / rules.length : 0;
+    return {
+        protocol: protocolName || path.basename(repoPath),
+        rules,
+        states: [...states],
+        sourceFiles: files,
+        totalPairs: allPairs.length,
+        avgConfidence: avgConf,
+        handWrittenOverlap: overlap,
+        novelRulesCount: extractedFns.size - overlap,
+    };
+}
+/**
+ * Convert enhanced rules to SSG-compatible StateAnnotation map.
+ */
+function enhancedRulesToMap(rules) {
+    const map = new Map();
+    for (const r of rules) {
+        map.set(r.function, {
+            pre_states: r.pre_states,
+            post_states: r.post_states,
+            invalidate: r.invalidate,
+        });
+    }
+    return map;
+}
+/**
+ * Measure the Discovery Rate impact of adding extracted protocol rules.
+ */
+async function measureDiscoveryImpact(extractedRules) {
+    // Baseline: current hand-written rules
+    const baselineAttr = await (0, evaluation_campaign_1.runFailureAttribution)();
+    const baselineBudget = (0, evaluation_campaign_1.computeErrorBudget)(baselineAttr);
+    const baselineDiscovery = (0, discovery_analytics_1.computeDiscoveryMetrics)(baselineAttr);
+    // Note: full integration requires running suggestAlternatives with merged rules
+    // For now, compare rule coverage
+    const defs = (0, protocol_coverage_1.loadDefaultProtocolDefinitions)();
+    const handWrittenFns = new Set();
+    for (const p of defs)
+        for (const fn of p.rules.keys())
+            handWrittenFns.add(fn);
+    const newFns = [...extractedRules.keys()].filter(fn => !handWrittenFns.has(fn));
+    return {
+        baseline: {
+            discoveryRate: baselineDiscovery.overall,
+            top3Rate: baselineBudget.successRate,
+            missingCandidate: baselineBudget.percentages.missing_candidate || 0,
+        },
+        rulesAdded: newFns.length,
+    };
+}
+function printFoundationReport(result, impact) {
+    console.log("\n╔════════════════════════════════════════════════════╗");
+    console.log("║   P6.0 Protocol Foundation Model                   ║");
+    console.log("╚════════════════════════════════════════════════════╝\n");
+    console.log(`Protocol:         ${result.protocol}`);
+    console.log(`Source Files:     ${result.sourceFiles.length}`);
+    console.log(`Call Pairs:       ${result.totalPairs}`);
+    console.log(`Rules Extracted:  ${result.rules.length}`);
+    console.log(`States Inferred:  ${result.states.length}`);
+    console.log(`Avg Confidence:   ${(result.avgConfidence * 100).toFixed(0)}%`);
+    console.log(`Hand-written Overlap: ${result.handWrittenOverlap} functions`);
+    console.log(`Novel Rules:      ${result.novelRulesCount}`);
+    console.log();
+    if (result.rules.length > 0) {
+        console.log("─── Top Extracted Rules ───");
+        console.log("Conf    Domain    Function              Pre → Post               Inv");
+        console.log("────────────────────────────────────────────────────────────────────");
+        for (const r of result.rules.slice(0, 15)) {
+            const conf = (r.confidence * 100).toFixed(0).padStart(4);
+            const dom = r.domain.padEnd(8);
+            const fn = r.function.padEnd(22);
+            const pre = `[${r.pre_states.join(",") || "none"}]`.padEnd(22);
+            const post = `[${r.post_states.join(",") || "none"}]`.padEnd(22);
+            const inv = r.invalidate ? `[${r.invalidate.join(",")}]` : "—";
+            console.log(`  ${conf}%  ${dom} ${fn} ${pre} → ${post} ${inv}`);
+        }
+        console.log();
+    }
+    if (impact) {
+        console.log("─── Discovery Impact ───");
+        console.log(`  Baseline Discovery:     ${(impact.baseline.discoveryRate * 100).toFixed(0)}%`);
+        console.log(`  Baseline Missing Cand:  ${(impact.baseline.missingCandidate * 100).toFixed(0)}%`);
+        console.log(`  New Rules Added:        ${impact.rulesAdded}`);
+        if (impact.rulesAdded > 0) {
+            console.log(`  → Potential discovery improvement from ${impact.rulesAdded} new protocol functions`);
+        }
+        console.log();
+    }
+}

package/dist/protocol-foundation.test.js

@@ -0,0 +1,163 @@
+"use strict";
+/**
+ * P6.0: Protocol Foundation Model Tests
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+const vitest_1 = require("vitest");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const protocol_foundation_1 = require("./protocol-foundation");
+const protocol_extractor_1 = require("./protocol-extractor");
+const FOUND_DIR = path.resolve(__dirname, "..", "test-protocol-foundation");
+fs.mkdirSync(FOUND_DIR, { recursive: true });
+function createTestRepo() {
+    const srcDir = path.join(FOUND_DIR, "src");
+    fs.mkdirSync(srcDir, { recursive: true });
+    // File protocol pattern
+    fs.writeFileSync(path.join(srcDir, "file_ops.c"), `
+    void read_config(const char* path) {
+        FILE* f = fopen(path, "r");
+        char buf[1024];
+        fread(buf, 1, 1024, f);
+        fclose(f);
+    }
+    void write_config(const char* path, const char* data) {
+        FILE* f = fopen(path, "w");
+        fwrite(data, 1, strlen(data), f);
+        fflush(f);
+        fclose(f);
+    }
+  `);
+    // DB protocol pattern
+    fs.writeFileSync(path.join(srcDir, "db_ops.js"), `
+    function queryUsers() {
+        const db = db_connect("localhost");
+        const rows = db_query(db, "SELECT * FROM users");
+        db_disconnect(db);
+    }
+    function insertLog(msg) {
+        const db = db_connect("localhost");
+        db_insert(db, "logs", msg);
+        db_disconnect(db);
+    }
+  `);
+    // Auth protocol pattern
+    fs.writeFileSync(path.join(srcDir, "auth_flow.c"), `
+    int authenticate(const char* user, const char* pass) {
+        if (!verify_password(user, pass)) return 0;
+        char* token = generate_jwt(user);
+        session_t* sess = create_session(token);
+        return sess ? 1 : 0;
+    }
+    void do_logout(session_t* sess) {
+        logout(sess);
+    }
+  `);
+    return FOUND_DIR;
+}
+(0, vitest_1.describe)("Protocol Foundation Model", () => {
+    createTestRepo();
+    (0, vitest_1.it)("infers intelligent state names", () => {
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("fopen", "post")).toBe("FILE_OPEN");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("fclose", "invalidate")).toBe("FILE_CLOSED");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("db_connect", "post")).toBe("DB_CONNECTED");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("verify_password", "post")).toBe("AUTH_VERIFIED");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("generate_jwt", "post")).toBe("AUTH_ISSUED");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("create_session", "post")).toBe("AUTH_CREATED");
+        (0, vitest_1.expect)((0, protocol_foundation_1.inferStateName)("logout", "invalidate")).toBe("AUTH_UNAUTHENTICATED");
+    });
+    (0, vitest_1.it)("infers enhanced rules with domain-specific states", () => {
+        const code = `
+      FILE* f = fopen("x", "r");
+      fread(buf, 1, 1024, f);
+      fclose(f);
+
+      DB* db = db_connect("localhost");
+      db_query(db, "SELECT 1");
+      db_disconnect(db);
+    `;
+        const pairs = (0, protocol_extractor_1.extractCallPairs)(code);
+        const rules = (0, protocol_foundation_1.inferEnhancedRules)(pairs, 1);
+        (0, vitest_1.expect)(rules.length).toBeGreaterThan(0);
+        // fopen should produce FILE_OPEN
+        const fopen = rules.find(r => r.function === "fopen");
+        (0, vitest_1.expect)(fopen).toBeDefined();
+        (0, vitest_1.expect)(fopen.domain).toBe("FILE");
+        (0, vitest_1.expect)(fopen.post_states).toContain("FILE_OPEN");
+        // fclose should invalidate FILE_OPEN
+        const fclose = rules.find(r => r.function === "fclose");
+        (0, vitest_1.expect)(fclose).toBeDefined();
+        (0, vitest_1.expect)(fclose.invalidate).toBeDefined();
+        // db_connect should produce DB_CONNECTED
+        const dbConn = rules.find(r => r.function === "db_connect");
+        (0, vitest_1.expect)(dbConn).toBeDefined();
+        (0, vitest_1.expect)(dbConn.domain).toBe("DB");
+    });
+    (0, vitest_1.it)("extracts protocol foundation from test repository", () => {
+        const result = (0, protocol_foundation_1.extractProtocolFoundation)(FOUND_DIR, "TestFoundation", 20, 1);
+        (0, vitest_1.expect)(result.rules.length).toBeGreaterThan(0);
+        (0, vitest_1.expect)(result.states.length).toBeGreaterThan(0);
+        (0, vitest_1.expect)(result.totalPairs).toBeGreaterThan(0);
+        (0, vitest_1.expect)(result.avgConfidence).toBeGreaterThan(0);
+        // Should have FILE states
+        (0, vitest_1.expect)(result.states.some(s => s.includes("FILE"))).toBe(true);
+        // Should have DB states
+        (0, vitest_1.expect)(result.states.some(s => s.includes("DB"))).toBe(true);
+        // Hand-written overlap: fopen/fread/fwrite/fclose match ground truth
+        (0, vitest_1.expect)(result.handWrittenOverlap).toBeGreaterThanOrEqual(2);
+        (0, protocol_foundation_1.printFoundationReport)(result);
+    });
+    (0, vitest_1.it)("converts enhanced rules to SSG-compatible map", () => {
+        const code = `FILE* f = fopen("x", "r"); fclose(f);`;
+        const pairs = (0, protocol_extractor_1.extractCallPairs)(code);
+        const rules = (0, protocol_foundation_1.inferEnhancedRules)(pairs, 1);
+        const map = (0, protocol_foundation_1.enhancedRulesToMap)(rules);
+        (0, vitest_1.expect)(map.size).toBeGreaterThan(0);
+        const fopenRule = map.get("fopen");
+        (0, vitest_1.expect)(fopenRule).toBeDefined();
+        (0, vitest_1.expect)(fopenRule.post_states.length).toBeGreaterThan(0);
+    });
+    (0, vitest_1.it)("measures discovery impact of extracted rules", async () => {
+        const code = `FILE* f = fopen("x", "r"); fclose(f);`;
+        const pairs = (0, protocol_extractor_1.extractCallPairs)(code);
+        const rules = (0, protocol_foundation_1.inferEnhancedRules)(pairs, 1);
+        const map = (0, protocol_foundation_1.enhancedRulesToMap)(rules);
+        const impact = await (0, protocol_foundation_1.measureDiscoveryImpact)(map);
+        (0, vitest_1.expect)(impact.baseline.discoveryRate).toBeGreaterThanOrEqual(0);
+        (0, vitest_1.expect)(impact.rulesAdded).toBeGreaterThanOrEqual(0);
+        (0, protocol_foundation_1.printFoundationReport)({ protocol: "test", rules, states: [], sourceFiles: [], totalPairs: pairs.length, avgConfidence: 1, handWrittenOverlap: 1, novelRulesCount: impact.rulesAdded }, impact);
+    }, 30000);
+});