progmune-runtime 2.1.6 → 3.2.0

package/dist/knowledge-evolution.js

@@ -0,0 +1,452 @@
+"use strict";
+/**
+ * Knowledge Evolution Pipeline
+ *
+ * Transforms the Knowledge Base from manual maintenance to a
+ * self-growing system: scan → discover → propose → review → accept.
+ *
+ * Usage:
+ *   npx ts-node src/knowledge-evolution.ts scan <repoPath>
+ *   npx ts-node src/knowledge-evolution.ts propose <repoPath>
+ *   npx ts-node src/knowledge-evolution.ts changelog
+ */
+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.scanRepo = scanRepo;
+exports.proposeUpdate = proposeUpdate;
+exports.generateFullChangelog = generateFullChangelog;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const protocol_detector_1 = require("./protocol-detector");
+const protocol_knowledge_1 = require("./protocol-knowledge");
+// ═══════════════════════════════════════════════════════════════
+// Step 1: Scan
+// ═══════════════════════════════════════════════════════════════
+function scanRepo(repoPath) {
+    const repoName = path.basename(repoPath);
+    const seqFile = path.join(path.dirname(repoPath), `${repoName}-sequences.json`);
+    if (!fs.existsSync(seqFile)) {
+        throw new Error(`No sequences file: ${seqFile}. Run C extraction first.`);
+    }
+    const sequences = JSON.parse(fs.readFileSync(seqFile, "utf-8"));
+    const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+    // Match against existing protocols
+    const existingMatches = [];
+    const matchedProtocols = new Set();
+    const unmatched = [];
+    for (const seq of sequences.slice(0, 50)) {
+        const result = (0, protocol_detector_1.validateProtocolState)(seq.calls || []);
+        for (const p of result.matchedProtocols) {
+            matchedProtocols.add(p);
+        }
+        if (result.matchedProtocols.length === 0) {
+            unmatched.push({
+                function: seq.function || "?",
+                calls: (seq.calls || []).slice(0, 8),
+                frequency: seq.totalCalls || 0,
+            });
+        }
+    }
+    for (const proto of matchedProtocols) {
+        const matchingSeqs = sequences.filter((s) => {
+            const r = (0, protocol_detector_1.validateProtocolState)(s.calls || []);
+            return r.matchedProtocols.includes(proto);
+        });
+        existingMatches.push({
+            protocol: proto,
+            sequenceCount: matchingSeqs.length,
+            examples: matchingSeqs.slice(0, 3).map((s) => (s.calls || []).slice(0, 5)),
+        });
+    }
+    // Generate proposal candidates from unmatched sequences
+    const candidates = generateProposals(unmatched, kb, repoName);
+    return {
+        repo: repoName,
+        timestamp: new Date().toISOString(),
+        totalSequences: sequences.length,
+        existingMatches,
+        unmatchedSequences: unmatched.slice(0, 20),
+        proposalCandidates: candidates,
+    };
+}
+function generateProposals(unmatched, kb, repoName) {
+    const candidates = [];
+    // Group unmatched functions by common prefixes
+    const groups = {};
+    for (const u of unmatched) {
+        // Find the closest existing protocol by call pattern similarity
+        for (const call of u.calls) {
+            for (const asset of kb.units) {
+                if (asset.steps.some(s => new RegExp(s.split(" ")[0] || "", "i").test(call))) {
+                    const key = asset.name;
+                    if (!groups[key])
+                        groups[key] = [];
+                    groups[key].push(call);
+                }
+            }
+        }
+    }
+    for (const [proto, calls] of Object.entries(groups)) {
+        if (calls.length >= 2) {
+            const uniqueCalls = [...new Set(calls)];
+            candidates.push({
+                protocolName: proto,
+                category: kb.units.find(a => a.name === proto)?.category || "connection",
+                newPatterns: uniqueCalls.slice(0, 5),
+                evidenceRepo: repoName,
+                evidenceSequences: unmatched.length,
+                suggestedAction: "extend",
+                confidence: Math.min(70, 30 + uniqueCalls.length * 10),
+            });
+        }
+    }
+    return candidates.slice(0, 5);
+}
+// ═══════════════════════════════════════════════════════════════
+// Step 2: Propose
+// ═══════════════════════════════════════════════════════════════
+function proposeUpdate(repoPath) {
+    const scan = scanRepo(repoPath);
+    const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+    const id = `PROPOSAL-${Date.now().toString(36)}`;
+    const changes = [];
+    // For each matched protocol, propose evidence addition
+    for (const match of scan.existingMatches) {
+        const asset = kb.units.find(a => a.name === match.protocol);
+        if (!asset)
+            continue;
+        const alreadyValidated = asset.validatedRepos.includes(scan.repo);
+        if (!alreadyValidated) {
+            changes.push({
+                assetId: asset.id,
+                assetName: asset.name,
+                action: "add_evidence",
+                before: { validatedRepos: [...asset.validatedRepos], validatedSequences: asset.validatedSequences, confidence: asset.confidence },
+                after: {
+                    validatedRepos: [...asset.validatedRepos, scan.repo],
+                    validatedSequences: asset.validatedSequences + scan.totalSequences,
+                    confidence: Math.min(95, asset.confidence + 5),
+                },
+                reason: `${scan.repo} sequences match ${asset.name} protocol (${match.sequenceCount}/50 sequences)`,
+            });
+        }
+    }
+    // For proposal candidates, suggest extensions
+    for (const cand of scan.proposalCandidates) {
+        const asset = kb.units.find(a => a.name === cand.protocolName);
+        if (!asset || cand.suggestedAction !== "extend")
+            continue;
+        changes.push({
+            assetId: asset.id,
+            assetName: asset.name,
+            action: "extend_patterns",
+            before: { confidence: asset.confidence },
+            after: { confidence: Math.min(90, asset.confidence + 8) },
+            reason: `${cand.evidenceRepo} found ${cand.newPatterns.length} new call patterns matching ${asset.name}: ${cand.newPatterns.join(", ")}`,
+            newPatterns: cand.newPatterns,
+        });
+    }
+    // Generate changelog
+    const changelog = generateChangelog(changes, scan.repo);
+    const proposal = {
+        id, timestamp: new Date().toISOString(), repo: scan.repo,
+        changes, changelog, status: "proposed",
+    };
+    // Save proposal for review
+    const proposalDir = ".progmune_corpus/proposals";
+    if (!fs.existsSync(proposalDir))
+        fs.mkdirSync(proposalDir, { recursive: true });
+    fs.writeFileSync(path.join(proposalDir, `${id}.json`), JSON.stringify(proposal, null, 2));
+    return proposal;
+}
+// ═══════════════════════════════════════════════════════════════
+// Step 3: Changelog
+// ═══════════════════════════════════════════════════════════════
+function generateChangelog(changes, repo) {
+    const lines = [];
+    lines.push(`# Knowledge Base Changelog`);
+    lines.push("");
+    lines.push(`**Source:** ${repo}`);
+    lines.push(`**Date:** ${new Date().toISOString().slice(0, 10)}`);
+    lines.push("");
+    for (const c of changes) {
+        lines.push(`## ${c.assetName} (${c.assetId})`);
+        lines.push("");
+        lines.push(`**Action:** ${c.action}`);
+        lines.push(`**Reason:** ${c.reason}`);
+        lines.push("");
+        if (c.before.confidence !== undefined && c.after.confidence !== undefined) {
+            lines.push(`| Metric | Before | After |`);
+            lines.push(`|--------|--------|-------|`);
+            lines.push(`| Confidence | ${c.before.confidence}% | ${c.after.confidence}% |`);
+            if (c.before.validatedRepos && c.after.validatedRepos) {
+                lines.push(`| Repos | ${c.before.validatedRepos.join(", ")} | ${c.after.validatedRepos.join(", ")} |`);
+            }
+            if (c.before.validatedSequences !== undefined && c.after.validatedSequences !== undefined) {
+                lines.push(`| Sequences | ${c.before.validatedSequences} | ${c.after.validatedSequences} |`);
+            }
+            lines.push("");
+        }
+        if (c.newPatterns) {
+            lines.push(`**New patterns:** \`${c.newPatterns.join("`, `")}\``);
+            lines.push("");
+        }
+    }
+    return lines.join("\n");
+}
+function formatUnitEvolution(unit) {
+    const l = [];
+    l.push(`\nKnowledge Evolution: ${unit.name} (${unit.id})`);
+    l.push(`Domain: ${unit.domain}  |  Maturity: ${unit.maturity}  |  Version: ${unit.currentVersion}`);
+    l.push(`Confidence: ${unit.confidence}%  |  RFC: ${unit.rfcReference || "none"}`);
+    l.push(`Repos: ${unit.validatedRepos.join(", ")}  |  Sequences: ${unit.validatedSequences}`);
+    l.push(`\nVersion History:`);
+    for (const v of unit.versionHistory) {
+        const f1Str = v.f1 !== undefined ? ` F1=${(v.f1 * 100).toFixed(0)}%` : "";
+        const reposStr = v.validatedRepos.length > 0 ? ` repos=[${v.validatedRepos.join(",")}]` : "";
+        const decisionIcon = v.decision?.outcome === "approved" ? "✅" : v.decision?.outcome === "rejected" ? "❌" : "↻";
+        l.push(`  ${decisionIcon} v${v.version} (${v.date}) → ${v.confidence}% conf, ${v.validatedSequences} seqs${reposStr}${f1Str}`);
+        l.push(`    ${v.notes}`);
+        if (v.decision) {
+            l.push(`    Decision: ${v.decision.outcome.toUpperCase()} by ${v.decision.decidedBy} — ${v.decision.reason}`);
+            l.push(`    Evidence: ${v.decision.evidence.join("; ")}`);
+        }
+    }
+    if (unit.concepts && unit.concepts.length > 0) {
+        l.push(`\nConcepts (${unit.concepts.length}):`);
+        for (const c of unit.concepts) {
+            l.push(`  ${c.name} (${c.required ? "required" : "optional"}) — ${c.description}`);
+            l.push(`    Constraints: ${c.constraints.join("; ")}`);
+        }
+    }
+    if (unit.relations && unit.relations.length > 0) {
+        l.push(`\nRelations:`);
+        for (const r of unit.relations) {
+            l.push(`  ${r.type} → ${r.targetId}: ${r.description}`);
+        }
+    }
+    if (unit.evidence && unit.evidence.length > 0) {
+        l.push(`\nEvidence (${unit.evidence.length}):`);
+        for (const e of unit.evidence) {
+            l.push(`  ${e.repo} (${e.type}): ${e.sequences} sequences, ${e.date}`);
+        }
+    }
+    l.push("");
+    return l.join("\n");
+}
+function generateFullChangelog() {
+    const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+    const lines = [];
+    lines.push("# Knowledge Base Full Changelog\n");
+    for (const asset of kb.units) {
+        lines.push(`## ${asset.name} (${asset.id})\n`);
+        lines.push(`**Current:** v${asset.currentVersion} · ${asset.maturity} · ${asset.confidence}% confidence\n`);
+        lines.push(`| Version | Date | Confidence | Repos | Seqs | Notes |`);
+        lines.push(`|---------|------|------------|-------|------|-------|`);
+        for (const v of asset.versionHistory) {
+            lines.push(`| v${v.version} | ${v.date} | ${v.confidence}% | ${v.validatedRepos.length} | ${v.validatedSequences} | ${v.notes} |`);
+        }
+        lines.push("");
+    }
+    return lines.join("\n");
+}
+// ═══════════════════════════════════════════════════════════════
+// CLI
+// ═══════════════════════════════════════════════════════════════
+if (require.main === module) {
+    const args = process.argv.slice(2);
+    const cmd = args[0];
+    const repoPath = args[1] ? path.resolve(args[1]) : ".";
+    const C = { r: "\x1b[0m", b: "\x1b[1m", d: "\x1b[2m", g: "\x1b[32m", y: "\x1b[33m", r2: "\x1b[31m", c: "\x1b[36m" };
+    if (cmd === "scan") {
+        console.error(`\n${C.b}${C.c}Scanning: ${repoPath}${C.r}\n`);
+        try {
+            const scan = scanRepo(repoPath);
+            console.log(`  Sequences: ${scan.totalSequences}`);
+            console.log(`  Matched protocols: ${scan.existingMatches.length}`);
+            for (const m of scan.existingMatches) {
+                console.log(`    ${C.g}${m.protocol}${C.r}: ${m.sequenceCount}/50 sequences`);
+                if (m.examples.length > 0)
+                    console.log(`      ${C.d}${m.examples[0].slice(0, 4).join(" → ")}${C.r}`);
+            }
+            console.log(`  Unmatched: ${scan.unmatchedSequences.length}`);
+            if (scan.unmatchedSequences.length > 0) {
+                console.log(`    ${C.y}Top patterns:${C.r}`);
+                for (const u of scan.unmatchedSequences.slice(0, 5)) {
+                    console.log(`      ${u.function} → ${u.calls.slice(0, 4).join(", ")}`);
+                }
+            }
+            console.log(`  Proposal candidates: ${scan.proposalCandidates.length}`);
+            for (const c of scan.proposalCandidates) {
+                console.log(`    ${c.protocolName}: ${c.suggestedAction} (${c.confidence}% confidence, ${c.evidenceSequences} evidence seqs)`);
+            }
+            console.log("");
+        }
+        catch (e) {
+            console.error(`${C.r2}❌ ${e.message}${C.r}`);
+            process.exit(1);
+        }
+    }
+    else if (cmd === "propose") {
+        console.error(`\n${C.b}${C.c}Generating proposal...${C.r}\n`);
+        try {
+            const proposal = proposeUpdate(repoPath);
+            console.log(`  Proposal: ${proposal.id}`);
+            console.log(`  Changes: ${proposal.changes.length}`);
+            for (const c of proposal.changes) {
+                console.log(`    ${c.action}: ${c.assetName} — ${c.reason.slice(0, 80)}`);
+            }
+            console.log(`\n${proposal.changelog}`);
+            console.log(`\n  ${C.y}Review: .progmune_corpus/proposals/${proposal.id}.json${C.r}`);
+            console.log(`  ${C.d}To accept: update src/protocol-knowledge.ts with proposed changes${C.r}\n`);
+        }
+        catch (e) {
+            console.error(`${C.r2}❌ ${e.message}${C.r}`);
+            process.exit(1);
+        }
+    }
+    else if (cmd === "diff") {
+        const unitId = args[1];
+        const v1 = args[2];
+        const v2 = args[3];
+        if (!unitId || !v1 || !v2) {
+            console.error("Usage: diff <unitId> <v1> <v2>");
+            process.exit(1);
+        }
+        const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+        const unit = kb.units.find(u => u.id === unitId || u.name === unitId);
+        if (!unit) {
+            console.error(`Unit not found: ${unitId}`);
+            process.exit(1);
+        }
+        const ver1 = unit.versionHistory.find((v) => v.version === v1);
+        const ver2 = unit.versionHistory.find((v) => v.version === v2);
+        if (!ver1 || !ver2) {
+            console.error("Version not found");
+            process.exit(1);
+        }
+        const C = { r: "\x1b[0m", b: "\x1b[1m", d: "\x1b[2m", g: "\x1b[32m", r2: "\x1b[31m", y: "\x1b[33m" };
+        const delta = (a, b) => `${b - a >= 0 ? "+" : ""}${b - a}`;
+        console.log(`\n${C.b}Knowledge Diff: ${unit.name}${C.r}`);
+        console.log(`${C.d}${v1} → ${v2}  (${ver1.date} → ${ver2.date})${C.r}\n`);
+        console.log(`  Confidence:    ${ver1.confidence}% → ${C.b}${ver2.confidence}%${C.r}  (${delta(ver1.confidence, ver2.confidence)}%)`);
+        console.log(`  Repos:         ${ver1.validatedRepos.length} → ${ver2.validatedRepos.length}  ${ver2.validatedRepos.filter((r) => !ver1.validatedRepos.includes(r)).length > 0 ? C.g + "+ " + ver2.validatedRepos.filter((r) => !ver1.validatedRepos.includes(r)).join(", ") + C.r : ""}`);
+        console.log(`  Sequences:     ${ver1.validatedSequences} → ${ver2.validatedSequences}  (${delta(ver1.validatedSequences, ver2.validatedSequences)})`);
+        if (ver1.f1 !== undefined && ver2.f1 !== undefined) {
+            const f1Delta = ver2.f1 - ver1.f1;
+            console.log(`  F1 Score:      ${(ver1.f1 * 100).toFixed(0)}% → ${(ver2.f1 * 100).toFixed(0)}%  (${f1Delta >= 0 ? "+" : ""}${(f1Delta * 100).toFixed(0)}pp)`);
+        }
+        if (ver1.precision !== undefined && ver2.precision !== undefined) {
+            console.log(`  Precision:     ${(ver1.precision * 100).toFixed(0)}% → ${(ver2.precision * 100).toFixed(0)}%`);
+        }
+        if (ver1.recall !== undefined && ver2.recall !== undefined) {
+            console.log(`  Recall:        ${(ver1.recall * 100).toFixed(0)}% → ${(ver2.recall * 100).toFixed(0)}%`);
+        }
+        // Concept changes
+        const v1Concepts = unit.concepts?.length || 0;
+        const v2Concepts = v1Concepts; // concepts tracked at unit level currently
+        console.log(`  Concepts:      ${v1Concepts} defined`);
+        // Decision trail
+        if (ver1.decision && ver2.decision) {
+            console.log(`\n  Decision Trail:`);
+            console.log(`  v${v1}: ${ver1.decision.outcome.toUpperCase()} by ${ver1.decision.decidedBy}`);
+            console.log(`  v${v2}: ${ver2.decision.outcome.toUpperCase()} by ${ver2.decision.decidedBy}`);
+        }
+        console.log(`\n  ${C.d}${ver2.notes}${C.r}\n`);
+    }
+    else if (cmd === "benchmark") {
+        const unitId = args[1];
+        if (!unitId) {
+            console.error("Usage: benchmark <unitId>");
+            process.exit(1);
+        }
+        const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+        const unit = kb.units.find(u => u.id === unitId || u.name === unitId);
+        if (!unit) {
+            console.error(`Unit not found: ${unitId}`);
+            process.exit(1);
+        }
+        console.log(`\n${unit.name} — Benchmark History`);
+        console.log(`Version   Date        F1     Prec   Recall  FP    FN    Confidence`);
+        console.log(`───────   ──────────  ─────  ─────  ─────  ────  ────  ──────────`);
+        for (const v of unit.versionHistory) {
+            const f1 = v.f1 !== undefined ? `${(v.f1 * 100).toFixed(0)}%`.padStart(5) : "  N/A ";
+            const p = v.precision !== undefined ? `${(v.precision * 100).toFixed(0)}%`.padStart(5) : "  N/A ";
+            const r = v.recall !== undefined ? `${(v.recall * 100).toFixed(0)}%`.padStart(5) : "  N/A ";
+            console.log(`v${v.version.padEnd(7)} ${v.date}  ${f1}  ${p}  ${r}  ${String(unit.fpHistory[unit.versionHistory.indexOf(v)] || "—").padStart(4)}  ${String(unit.fnHistory[unit.versionHistory.indexOf(v)] || "—").padStart(4)}  ${v.confidence}%`);
+        }
+        const first = unit.versionHistory[0];
+        const last = unit.versionHistory[unit.versionHistory.length - 1];
+        if (first.f1 !== undefined && last.f1 !== undefined) {
+            console.log(`\n  F1 improvement: ${(first.f1 * 100).toFixed(0)}% → ${(last.f1 * 100).toFixed(0)}% (${last.f1 > first.f1 ? "+" : ""}${((last.f1 - first.f1) * 100).toFixed(0)}pp)`);
+        }
+        console.log("");
+    }
+    else if (cmd === "changelog") {
+        const unitFilter = args.includes("--unit") ? args[args.indexOf("--unit") + 1] : undefined;
+        if (unitFilter) {
+            const kb = (0, protocol_knowledge_1.buildKnowledgeBase)();
+            const unit = kb.units.find(u => u.id === unitFilter || u.name === unitFilter);
+            if (!unit) {
+                console.error(`Unit not found: ${unitFilter}`);
+                process.exit(1);
+            }
+            console.log(formatUnitEvolution(unit));
+        }
+        else {
+            console.log(generateFullChangelog());
+        }
+    }
+    else {
+        console.log(`
+${C.b}Knowledge Evolution Pipeline${C.r}
+
+${C.d}Usage:${C.r}
+  npx ts-node src/knowledge-evolution.ts scan <repoPath>
+      Scan a repo, match protocols, discover new patterns
+
+  npx ts-node src/knowledge-evolution.ts propose <repoPath>
+      Generate a Knowledge Base update proposal with changelog
+
+  npx ts-node src/knowledge-evolution.ts changelog
+      Show full Knowledge Base version history
+
+${C.d}Examples:${C.r}
+  npx ts-node src/knowledge-evolution.ts scan benchmarks/nginx
+  npx ts-node src/knowledge-evolution.ts propose benchmarks/nghttp2
+  npx ts-node src/knowledge-evolution.ts changelog
+    `);
+    }
+}