@pella-labs/pinakes 0.3.14 → 0.4.0

package/dist/cli/contradiction.js

@@ -1,15 +1,38 @@
+/**
+ * Contradiction detector v2 (D41 — topic-clustered claim comparison).
+ *
+ * Two-phase pipeline:
+ *   Phase A (claims.ts): Per-file LLM extraction of {topic, claims[]}
+ *   Phase B (this file): Group claims by topic, compare cross-file via LLM
+ *
+ * Topic dedup uses embedding cosine similarity > threshold (default 0.85)
+ * to merge terminology variants like "OAuth2" / "OAuth 2.0".
+ */
 import { writeFileSync } from 'node:fs';
 import { join } from 'node:path';
 import { logger } from '../observability/logger.js';
-const RATE_LIMIT_MS = 0; // disabled during testing (was 60 * 60 * 1000)
-const MAX_PAIRS = 50;
-const SIMILARITY_THRESHOLD = 0.3;
-const JUDGE_SYSTEM = `You are a contradiction detector. Given two text chunks from a knowledge wiki, determine if they contain contradictory claims. Respond with ONLY valid JSON: {"contradicts": true/false, "explanation": "why", "confidence": "high"|"medium"|"low"}. Only report contradictions you are confident about.`;
+const RATE_LIMIT_MS = 60 * 60 * 1000; // 1 hour
+const DEFAULT_TOPIC_SIMILARITY = 0.85;
+const COMPARE_SYSTEM = `You are a contradiction detector for a knowledge wiki. Given claims about a topic from different wiki files, identify any contradictions — places where two files make incompatible factual statements.
+
+Return ONLY valid JSON:
+{"contradictions":[{"claim_a":"exact claim text","source_a":"file","claim_b":"exact claim text","source_b":"file","explanation":"why these contradict","confidence":"high"|"medium"}]}
+
+Rules:
+- Only report genuine factual contradictions, not differences in emphasis or scope
+- "high" confidence = clear logical incompatibility
+- "medium" confidence = likely contradiction but could be context-dependent
+- If no contradictions, return {"contradictions":[]}`;
+// ----------------------------------------------------------------------------
+// Main entry point
+// ----------------------------------------------------------------------------
 /**
- * Run a contradiction scan. Returns immediately if rate-limited.
+ * Run contradiction scan using topic-clustered claim comparison (D41).
+ * Requires claims to be extracted first (via extractAllClaims).
  */
 export async function contradictionScan(opts) {
-    const { bundle, scope, llmProvider, wikiRoot } = opts;
+    const { bundle, scope, llmProvider, wikiRoot, progress } = opts;
+    const threshold = opts.topicSimilarity ?? DEFAULT_TOPIC_SIMILARITY;
     // Rate limit check
     const lastScan = bundle.writer
         .prepare(`SELECT value FROM pinakes_meta WHERE key = ?`)
@@ -17,157 +40,201 @@ export async function contradictionScan(opts) {
     if (lastScan) {
         const lastTs = parseInt(lastScan.value, 10);
         if (Date.now() - lastTs < RATE_LIMIT_MS) {
-            return { scanned_pairs: 0, contradictions: [], rate_limited: true };
+            return { scanned_pairs: 0, topics_scanned: 0, claims_extracted: 0, contradictions: [], rate_limited: true };
         }
     }
-    if (!llmProvider.available()) {
-        throw new Error('No LLM provider available for contradiction detection. ' +
-            'Set PINAKES_OLLAMA_URL, ANTHROPIC_API_KEY, or OPENAI_API_KEY, ' +
-            'or install the claude/codex CLI.');
+    // Get all claims grouped by topic
+    const allClaims = bundle.writer
+        .prepare(`SELECT topic, claim, source_uri FROM pinakes_claims WHERE scope = ? ORDER BY topic`)
+        .all(scope);
+    if (allClaims.length === 0) {
+        return { scanned_pairs: 0, topics_scanned: 0, claims_extracted: 0, contradictions: [], rate_limited: false };
+    }
+    // Group claims by topic
+    let topicGroups = groupByTopic(allClaims);
+    // Topic dedup via embeddings (merge "OAuth2" and "OAuth 2.0")
+    if (opts.embedder) {
+        topicGroups = await deduplicateTopics(topicGroups, opts.embedder, threshold);
     }
-    // Find candidate pairs via vector similarity
-    const pairs = findCandidatePairs(bundle, scope);
+    // Filter to topics with claims from 2+ files (cross-file contradictions only)
+    const crossFileTopics = topicGroups.filter((g) => {
+        const uniqueFiles = new Set(g.claims.map((c) => c.source_uri));
+        return uniqueFiles.size >= 2;
+    });
     const contradictions = [];
     let scanned = 0;
-    for (const pair of pairs) {
+    progress?.startPhase('Phase 1/3: Comparing claims across topics', crossFileTopics.length);
+    for (const group of crossFileTopics) {
+        const uniqueFiles = new Set(group.claims.map((c) => c.source_uri));
         try {
+            const prompt = formatComparisonPrompt(group);
             const response = await llmProvider.complete({
-                system: JUDGE_SYSTEM,
-                prompt: `Chunk A (from ${pair.a.source_uri}):\n${pair.a.text}\n\nChunk B (from ${pair.b.source_uri}):\n${pair.b.text}`,
-                maxTokens: 200,
+                system: COMPARE_SYSTEM,
+                prompt,
+                maxTokens: 500,
             });
-            const judgment = parseJudgment(response);
-            if (judgment && judgment.contradicts && (judgment.confidence === 'high' || judgment.confidence === 'medium')) {
+            const parsed = parseContradictionResponse(response);
+            for (const c of parsed) {
                 contradictions.push({
-                    chunkA: pair.a,
-                    chunkB: pair.b,
-                    explanation: judgment.explanation,
-                    confidence: judgment.confidence,
+                    topic: group.topic,
+                    claimA: { claim: c.claim_a, source_uri: c.source_a },
+                    claimB: { claim: c.claim_b, source_uri: c.source_b },
+                    explanation: c.explanation,
+                    confidence: c.confidence,
                 });
             }
             scanned++;
+            progress?.tick(group.topic, `${group.claims.length} claims from ${uniqueFiles.size} files — ${parsed.length > 0 ? `${parsed.length} CONTRADICTION(S)` : 'clean'}`);
         }
         catch (err) {
-            logger.warn({ err, pairA: pair.a.id, pairB: pair.b.id }, 'contradiction check failed for pair');
+            logger.warn({ err, topic: group.topic }, 'contradiction comparison failed for topic');
+            progress?.tick(group.topic, `failed: ${err instanceof Error ? err.message.slice(0, 60) : err}`);
         }
     }
+    progress?.endPhase(`${contradictions.length} contradictions found across ${scanned} topics`);
     // Update rate limit timestamp
     bundle.writer
         .prepare(`INSERT OR REPLACE INTO pinakes_meta (key, value) VALUES ('last_contradiction_scan', ?)`)
         .run(String(Date.now()));
-    // Write contradictions.md if any found
+    // Write report if contradictions found
     if (contradictions.length > 0) {
-        writeContradictionReport(wikiRoot, contradictions, bundle, scope);
+        writeContradictionReport(wikiRoot, contradictions);
     }
-    return { scanned_pairs: scanned, contradictions, rate_limited: false };
+    return {
+        scanned_pairs: scanned,
+        topics_scanned: crossFileTopics.length,
+        claims_extracted: allClaims.length,
+        contradictions,
+        rate_limited: false,
+    };
+}
+function groupByTopic(claims) {
+    const map = new Map();
+    for (const c of claims) {
+        const key = c.topic.toLowerCase();
+        let group = map.get(key);
+        if (!group) {
+            group = { topic: c.topic, claims: [] };
+            map.set(key, group);
+        }
+        group.claims.push({ claim: c.claim, source_uri: c.source_uri });
+    }
+    return [...map.values()];
 }
 /**
- * Find candidate pairs for contradiction checking.
- * Uses vector similarity to find chunks that are semantically similar
- * (which is a prerequisite for them to potentially contradict).
+ * Merge topic groups whose topic strings are semantically similar
+ * (cosine similarity > threshold). Handles "OAuth2" / "OAuth 2.0" merging.
  */
-function findCandidatePairs(bundle, scope) {
-    // Get all chunks with their vec embeddings
-    const chunks = bundle.writer
-        .prepare(`SELECT c.id, n.source_uri, c.text, c.rowid
-       FROM pinakes_chunks c
-       JOIN pinakes_nodes n ON c.node_id = n.id
-       WHERE n.scope = ?
-       ORDER BY c.rowid`)
-        .all(scope);
-    if (chunks.length < 2)
-        return [];
-    // For each chunk, find the top 5 most similar via vec
-    const pairs = new Set();
-    const result = [];
-    for (const chunk of chunks) {
-        if (result.length >= MAX_PAIRS)
-            break;
-        const similar = bundle.writer
-            .prepare(`SELECT rowid, distance
-         FROM pinakes_chunks_vec
-         WHERE embedding MATCH (SELECT embedding FROM pinakes_chunks_vec WHERE rowid = ?)
-         AND k = ?
-         ORDER BY distance`)
-            .all(chunk.rowid, 6); // 6 because first result is self
-        for (const sim of similar) {
-            if (sim.rowid === chunk.rowid)
-                continue;
-            if (sim.distance > SIMILARITY_THRESHOLD)
-                continue;
-            // Deduplicate symmetric pairs
-            const pairKey = [chunk.rowid, sim.rowid].sort().join(':');
-            if (pairs.has(pairKey))
-                continue;
-            pairs.add(pairKey);
-            const other = chunks.find((c) => c.rowid === sim.rowid);
-            if (!other)
-                continue;
-            // Skip same-source pairs (they're likely just adjacent sections)
-            if (chunk.source_uri === other.source_uri)
-                continue;
-            result.push({
-                a: { id: chunk.id, source_uri: chunk.source_uri, text: chunk.text },
-                b: { id: other.id, source_uri: other.source_uri, text: other.text },
-            });
-            if (result.length >= MAX_PAIRS)
-                break;
+export async function deduplicateTopics(groups, embedder, threshold) {
+    if (groups.length <= 1)
+        return groups;
+    // Embed all topic strings
+    const embeddings = [];
+    for (const g of groups) {
+        embeddings.push(await embedder.embed(g.topic));
+    }
+    // Union-find for merging
+    const parent = groups.map((_, i) => i);
+    function find(i) {
+        while (parent[i] !== i) {
+            parent[i] = parent[parent[i]];
+            i = parent[i];
+        }
+        return i;
+    }
+    function union(a, b) {
+        parent[find(b)] = find(a);
+    }
+    // Compare all pairs
+    for (let i = 0; i < groups.length; i++) {
+        for (let j = i + 1; j < groups.length; j++) {
+            const sim = cosineSimilarity(embeddings[i], embeddings[j]);
+            if (sim > threshold) {
+                union(i, j);
+            }
         }
     }
-    return result;
+    // Merge groups
+    const merged = new Map();
+    for (let i = 0; i < groups.length; i++) {
+        const root = find(i);
+        let target = merged.get(root);
+        if (!target) {
+            target = { topic: groups[root].topic, claims: [] };
+            merged.set(root, target);
+        }
+        target.claims.push(...groups[i].claims);
+    }
+    return [...merged.values()];
+}
+function cosineSimilarity(a, b) {
+    let dot = 0, normA = 0, normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        dot += a[i] * b[i];
+        normA += a[i] * a[i];
+        normB += b[i] * b[i];
+    }
+    const denom = Math.sqrt(normA) * Math.sqrt(normB);
+    return denom === 0 ? 0 : dot / denom;
 }
-function parseJudgment(response) {
+// ----------------------------------------------------------------------------
+// LLM prompt + response parsing
+// ----------------------------------------------------------------------------
+function formatComparisonPrompt(group) {
+    const lines = [`Topic: "${group.topic}"\n\nClaims from different files:\n`];
+    for (const c of group.claims) {
+        lines.push(`- [${c.source_uri}]: "${c.claim}"`);
+    }
+    return lines.join('\n');
+}
+export function parseContradictionResponse(response) {
     try {
-        const match = response.match(/\{[\s\S]*\}/);
-        if (!match)
-            return null;
-        const parsed = JSON.parse(match[0]);
-        if (typeof parsed.contradicts !== 'boolean')
-            return null;
-        return {
-            contradicts: parsed.contradicts,
-            explanation: parsed.explanation ?? '',
-            confidence: parsed.confidence ?? 'low',
-        };
+        const fenceMatch = response.match(/```(?:json)?\s*\n?([\s\S]*?)\n?```/);
+        const jsonStr = fenceMatch ? fenceMatch[1] : response;
+        const objMatch = jsonStr.match(/\{[\s\S]*\}/);
+        if (!objMatch)
+            return [];
+        const parsed = JSON.parse(objMatch[0]);
+        if (!Array.isArray(parsed.contradictions))
+            return [];
+        return parsed.contradictions.filter((c) => typeof c.claim_a === 'string' &&
+            typeof c.claim_b === 'string' &&
+            typeof c.explanation === 'string' &&
+            (c.confidence === 'high' || c.confidence === 'medium'));
     }
     catch {
-        return null;
+        return [];
     }
 }
-function writeContradictionReport(wikiRoot, contradictions, bundle, scope) {
-    // writeFileSync and join imported at top level
+// ----------------------------------------------------------------------------
+// Report output
+// ----------------------------------------------------------------------------
+function writeContradictionReport(wikiRoot, contradictions) {
     const lines = [
         '# Detected Contradictions',
         '',
         `*Last scanned: ${new Date().toISOString()}*`,
         '',
     ];
+    // Group by topic
+    const byTopic = new Map();
     for (const c of contradictions) {
-        lines.push(`## ${c.chunkA.source_uri} vs ${c.chunkB.source_uri}`);
-        lines.push('');
-        lines.push(`- **Chunk A** (${c.chunkA.source_uri}): "${truncate(c.chunkA.text, 200)}"`);
-        lines.push(`- **Chunk B** (${c.chunkB.source_uri}): "${truncate(c.chunkB.text, 200)}"`);
-        lines.push(`- **Explanation**: ${c.explanation}`);
-        lines.push(`- **Confidence**: ${c.confidence}`);
+        const list = byTopic.get(c.topic) ?? [];
+        list.push(c);
+        byTopic.set(c.topic, list);
+    }
+    for (const [topic, items] of byTopic) {
+        lines.push(`## ${topic}`);
         lines.push('');
+        for (const c of items) {
+            lines.push(`- **${c.claimA.source_uri}**: "${c.claimA.claim}"`);
+            lines.push(`- **${c.claimB.source_uri}**: "${c.claimB.claim}"`);
+            lines.push(`- **Explanation**: ${c.explanation} (${c.confidence} confidence)`);
+            lines.push('');
+        }
     }
     writeFileSync(join(wikiRoot, 'contradictions.md'), lines.join('\n'), 'utf8');
-    // Log the scan
-    try {
-        bundle.writer
-            .prepare(`INSERT INTO pinakes_log (ts, scope, kind, source_uri, payload)
-         VALUES (?, ?, 'contradiction:scan', NULL, ?)`)
-            .run(Date.now(), scope, JSON.stringify({ contradictions_found: contradictions.length }));
-    }
-    catch {
-        // Non-fatal
-    }
-}
-function truncate(s, maxLen) {
-    if (s.length <= maxLen)
-        return s;
-    return s.slice(0, maxLen) + '...';
 }
-// Export for testing
-export { findCandidatePairs as _findCandidatePairs, parseJudgment as _parseJudgment };
+// Export internals for testing
+export { groupByTopic as _groupByTopic, cosineSimilarity as _cosineSimilarity };
 //# sourceMappingURL=contradiction.js.map

package/dist/cli/contradiction.js.map

@@ -1 +1 @@
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package/dist/cli/index.js

@@ -49,7 +49,9 @@ function getRequiredString(flags, key) {
     return v;
 }
 async function main() {
-    const argv = process.argv.slice(2);
+    const rawArgv = process.argv.slice(2);
+    // Skip leading '--' from pnpm's argument separator (pnpm run pinakes -- serve)
+    const argv = rawArgv[0] === '--' ? rawArgv.slice(1) : rawArgv;
     const subcommand = argv[0];
     const { flags } = parseFlags(argv.slice(1));
     switch (subcommand) {
@@ -106,7 +108,7 @@ async function main() {
             });
             // eslint-disable-next-line no-console
             console.log(`\nAudit complete: ${result.contradictions.contradictions.length} contradictions, ` +
-                `${result.gaps_found} gaps, ${result.stub_pages_created.length} stub pages created.`);
+                `${result.gaps_found} gaps, ${result.topology_gaps} topology gaps.`);
             break;
         }
         case 'clean-wiki': {

package/dist/cli/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AACA,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAC;AAC7E,OAAO,EACL,UAAU,EACV,eAAe,IAAI,sBAAsB,GAC1C,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACvD,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AAC9C,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAC1C,OAAO,EAAE,MAAM,EAAE,MAAM,4BAA4B,CAAC;AAgBpD,SAAS,UAAU,CAAC,IAAc;IAChC,MAAM,KAAK,GAAU,EAAE,CAAC;IACxB,MAAM,UAAU,GAAa,EAAE,CAAC;IAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAE,CAAC;QACrB,IAAI,GAAG,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YAC/B,IAAI,KAAK,GAAG,CAAC,EAAE,CAAC;gBACd,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;YACpD,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBACzB,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;oBACnC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC;oBAC3B,CAAC,EAAE,CAAC;gBACN,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACvB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,CAAC;AAC/B,CAAC;AAED,SAAS,SAAS,CAAC,KAAY,EAAE,GAAW;IAC1C,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC;IACrB,OAAO,OAAO,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;AAC/C,CAAC;AAED,SAAS,iBAAiB,CAAC,KAAY,EAAE,GAAW;IAClD,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAChC,IAAI,CAAC,CAAC;QAAE,MAAM,IAAI,KAAK,CAAC,4BAA4B,GAAG,EAAE,CAAC,CAAC;IAC3D,OAAO,CAAC,CAAC;AACX,CAAC;AAED,KAAK,UAAU,IAAI;IACjB,MAAM,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACtC,+EAA+E;IAC/E,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;IAC9D,MAAM,UAAU,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;IAC3B,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;IAE5C,QAAQ,UAAU,EAAE,CAAC;QACnB,KAAK,OAAO,CAAC,CAAC,CAAC;YACb,MAAM,YAAY,CAAC;gBACjB,WAAW,EAAE,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC;gBAC7C,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;gBACnC,WAAW,EAAE,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC;gBAC7C,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,iBAAiB,CAAC;aACnD,CAAC,CAAC;YACH,MAAM;QACR,CAAC;QAED,KAAK,SAAS,CAAC,CAAC,CAAC;YACf,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,EAAE,OAAO,CAIzB,CAAC;YACd,MAAM,SAAS,GAAG,MAAM,cAAc,CAAC;gBACrC,WAAW,EAAE,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC;gBAC7C,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;gBACnC,WAAW,EAAE,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC;gBAC7C,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,iBAAiB,CAAC;gBAClD,KAAK;aACN,CAAC,CAAC;YACH,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,sCAAsC;gBACtC,OAAO,CAAC,GAAG,CACT,GAAG,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,KAAK,UAAU,CAAC,CAAC,KAAK,GAAG;oBACvD,gBAAgB,CAAC,CAAC,YAAY,mBAAmB,CAAC,CAAC,cAAc,GAAG;oBACpE,kBAAkB,CAAC,CAAC,cAAc,aAAa,CAAC,CAAC,UAAU,IAAI,CAClE,CAAC;YACJ,CAAC;YACD,MAAM;QACR,CAAC;QAED,KAAK,QAAQ,CAAC,CAAC,CAAC;YACd,MAAM,QAAQ,GAAG,aAAa,CAAC;gBAC7B,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;gBACnC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,iBAAiB,CAAC;aACnD,CAAC,CAAC;YACH,sCAAsC;YACtC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC;YACpC,MAAM;QACR,CAAC;QAED,KAAK,OAAO,CAAC,CAAC,CAAC;YACb,MAAM,IAAI,GAAG,YAAY,CAAC;gBACxB,CAAC,EAAE,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,KAAK,EAAE,GAAG,CAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;gBAC3E,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;gBACnC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,iBAAiB,CAAC;gBAClD,KAAK,EAAG,SAAS,CAAC,KAAK,EAAE,OAAO,CAA4B,IAAI,SAAS;aAC1E,CAAC,CAAC;YACH,sCAAsC;YACtC,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC;YAC/B,MAAM;QACR,CAAC;QAED,KAAK,YAAY,CAAC,CAAC,CAAC;YAClB,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC;gBACpC,WAAW,EAAE,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC;gBAC7C,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;aACpC,CAAC,CAAC;YACH,sCAAsC;YACtC,OAAO,CAAC,GAAG,CACT,qBAAqB,MAAM,CAAC,cAAc,CAAC,cAAc,CAAC,MAAM,mBAAmB;gBACjF,GAAG,MAAM,CAAC,UAAU,UAAU,MAAM,CAAC,aAAa,iBAAiB,CACtE,CAAC;YACF,MAAM;QACR,CAAC;QAED,KAAK,YAAY,CAAC,CAAC,CAAC;YAClB,MAAM,WAAW,GAAG,UAAU,CAAC,SAAS,CAAC,KAAK,EAAE,cAAc,CAAC,IAAI,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC;YAClF,MAAM,QAAQ,GAAG,sBAAsB,CAAC,WAAW,CAAC,CAAC;YACrD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAC;YACjD,MAAM,OAAO,GAAG,oBAAoB,CAAC,WAAW,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAC;YACtE,sCAAsC;YACtC,OAAO,CAAC,GAAG,CAAC,WAAW,OAAO,6BAA6B,CAAC,CAAC;YAC7D,MAAM;QACR,CAAC;QAED,KAAK,OAAO,CAAC,CAAC,CAAC;YACb,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,EAAE,OAAO,CAA2B,CAAC;YAC1E,MAAM,MAAM,GAAG,YAAY,CAAC;gBAC1B,KAAK;gBACL,OAAO,EAAE,KAAK,CAAC,SAAS,CAAC,KAAK,IAAI;gBAClC,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC;gBACnC,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package/dist/cli/progress.d.ts

@@ -0,0 +1,19 @@
+/**
+ * Progress reporter for long-running CLI operations (D44).
+ *
+ * Writes phase headers and per-item progress to stderr so it doesn't
+ * interfere with structured stdout output or piping.
+ */
+export interface ProgressReporter {
+    startPhase(name: string, total: number): void;
+    tick(label: string, detail?: string): void;
+    endPhase(summary: string): void;
+}
+/**
+ * Create a progress reporter that writes to stderr.
+ * Pass `quiet: true` to suppress all output (for tests or non-TTY).
+ */
+export declare function createProgressReporter(opts?: {
+    quiet?: boolean;
+}): ProgressReporter;
+//# sourceMappingURL=progress.d.ts.map

package/dist/cli/progress.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"progress.d.ts","sourceRoot":"","sources":["../../src/cli/progress.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,WAAW,gBAAgB;IAC/B,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9C,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3C,QAAQ,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;CACjC;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,gBAAgB,CAkCnF"}

package/dist/cli/progress.js

@@ -0,0 +1,44 @@
+/**
+ * Progress reporter for long-running CLI operations (D44).
+ *
+ * Writes phase headers and per-item progress to stderr so it doesn't
+ * interfere with structured stdout output or piping.
+ */
+/**
+ * Create a progress reporter that writes to stderr.
+ * Pass `quiet: true` to suppress all output (for tests or non-TTY).
+ */
+export function createProgressReporter(opts) {
+    const quiet = opts?.quiet ?? false;
+    let phaseStart = 0;
+    let current = 0;
+    let total = 0;
+    return {
+        startPhase(name, count) {
+            total = count;
+            current = 0;
+            phaseStart = Date.now();
+            if (!quiet) {
+                process.stderr.write(`${name} (${count} items)...\n`);
+            }
+        },
+        tick(label, detail) {
+            current++;
+            if (!quiet) {
+                const elapsed = ((Date.now() - phaseStart) / 1000).toFixed(1);
+                const parts = [`  [${current}/${total}] ${label}`];
+                if (detail)
+                    parts.push(` — ${detail}`);
+                parts.push(` (${elapsed}s)`);
+                process.stderr.write(parts.join('') + '\n');
+            }
+        },
+        endPhase(summary) {
+            if (!quiet) {
+                const elapsed = ((Date.now() - phaseStart) / 1000).toFixed(1);
+                process.stderr.write(`  ${summary} (${elapsed}s total)\n\n`);
+            }
+        },
+    };
+}
+//# sourceMappingURL=progress.js.map

package/dist/cli/progress.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"progress.js","sourceRoot":"","sources":["../../src/cli/progress.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAQH;;;GAGG;AACH,MAAM,UAAU,sBAAsB,CAAC,IAA0B;IAC/D,MAAM,KAAK,GAAG,IAAI,EAAE,KAAK,IAAI,KAAK,CAAC;IACnC,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,IAAI,KAAK,GAAG,CAAC,CAAC;IAEd,OAAO;QACL,UAAU,CAAC,IAAY,EAAE,KAAa;YACpC,KAAK,GAAG,KAAK,CAAC;YACd,OAAO,GAAG,CAAC,CAAC;YACZ,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACxB,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,IAAI,KAAK,KAAK,cAAc,CAAC,CAAC;YACxD,CAAC;QACH,CAAC;QAED,IAAI,CAAC,KAAa,EAAE,MAAe;YACjC,OAAO,EAAE,CAAC;YACV,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAC,GAAG,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;gBAC9D,MAAM,KAAK,GAAG,CAAC,MAAM,OAAO,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC,CAAC;gBACnD,IAAI,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,MAAM,MAAM,EAAE,CAAC,CAAC;gBACvC,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,IAAI,CAAC,CAAC;gBAC7B,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC;YAC9C,CAAC;QACH,CAAC;QAED,QAAQ,CAAC,OAAe;YACtB,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAC,GAAG,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;gBAC9D,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,OAAO,KAAK,OAAO,cAAc,CAAC,CAAC;YAC/D,CAAC;QACH,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/cli/serve.js

@@ -138,7 +138,7 @@ export async function buildServer(options) {
         'Only fall back to Grep/Read/Glob after checking the knowledge base, or when you need ' +
         'to find exact symbols, read specific source files, or make code changes. ' +
         `Use \`${executeToolName}\` for advanced operations: graph traversal, gap detection, writing new knowledge.`;
-    const mcp = new McpServer({ name: serverName, version: '0.3.14' }, { capabilities: { tools: {} }, instructions });
+    const mcp = new McpServer({ name: serverName, version: '0.3.15' }, { capabilities: { tools: {} }, instructions });
     mcp.registerTool(searchToolName, searchToolConfig, instrumentHandler(searchToolName, makeSearchHandler({
         repository, embedder, bundle: projectBundle,
         personalBundle: personalBundle ?? undefined,

package/dist/db/client.js

@@ -121,7 +121,7 @@ export function openDb(path, options = {}) {
     if (runMigrations) {
         writer
             .prepare('INSERT OR IGNORE INTO pinakes_meta (key, value) VALUES (?, ?)')
-            .run('schema_version', '2');
+            .run('schema_version', '3');
     }
     logger.info({ path: absPath, sqliteVersion: versionRow.v }, 'opened SQLite db');
     return { path: absPath, writer, readers, drizzleWriter };

package/dist/db/migrations/0003_add_pinakes_claims.sql

@@ -0,0 +1,13 @@
+CREATE TABLE `pinakes_claims` (
+	`id` integer PRIMARY KEY AUTOINCREMENT NOT NULL,
+	`scope` text NOT NULL,
+	`source_uri` text NOT NULL,
+	`chunk_id` text REFERENCES `pinakes_chunks`(`id`) ON DELETE SET NULL,
+	`topic` text NOT NULL,
+	`claim` text NOT NULL,
+	`extracted_at` integer NOT NULL
+);
+--> statement-breakpoint
+CREATE INDEX `idx_claims_topic` ON `pinakes_claims` (`scope`,`topic`);
+--> statement-breakpoint
+CREATE INDEX `idx_claims_source` ON `pinakes_claims` (`scope`,`source_uri`);

package/dist/db/migrations/0004_add_confidence_score.sql

@@ -0,0 +1,12 @@
+-- Phase 11.1: Add numeric confidence_score with time decay support (D50)
+-- The TEXT confidence column is PRESERVED for backward compatibility.
+
+ALTER TABLE `pinakes_nodes` ADD `confidence_score` real NOT NULL DEFAULT 0.7;--> statement-breakpoint
+
+-- Backfill from existing TEXT confidence column
+UPDATE `pinakes_nodes` SET `confidence_score` = CASE `confidence`
+  WHEN 'extracted' THEN 0.7
+  WHEN 'inferred' THEN 0.5
+  WHEN 'ambiguous' THEN 0.3
+  ELSE 0.7
+END;

package/dist/db/migrations/meta/_journal.json

@@ -22,6 +22,20 @@
       "when": 1776192000000,
       "tag": "0002_rename_kg_to_pinakes",
       "breakpoints": true
+    },
+    {
+      "idx": 3,
+      "version": "6",
+      "when": 1776134400000,
+      "tag": "0003_add_pinakes_claims",
+      "breakpoints": true
+    },
+    {
+      "idx": 4,
+      "version": "6",
+      "when": 1776220800000,
+      "tag": "0004_add_confidence_score",
+      "breakpoints": true
     }
   ]
 }