@pella-labs/pinakes 0.1.9 → 0.2.0

package/dist/cli/contradiction-cli.d.ts

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+import { type ContradictionResult } from './contradiction.js';
+/**
+ * CLI wrapper for the contradiction scan command.
+ * Sets up DB connection and LLM provider, runs the scan, cleans up.
+ */
+export declare function contradictionScanCommand(opts: {
+    scope: 'project' | 'personal';
+    wikiPath?: string;
+    dbPath?: string;
+}): Promise<ContradictionResult>;
+//# sourceMappingURL=contradiction-cli.d.ts.map

package/dist/cli/contradiction-cli.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"contradiction-cli.d.ts","sourceRoot":"","sources":["../../src/cli/contradiction-cli.ts"],"names":[],"mappings":"AAGA,OAAO,EAAqB,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAEjF;;;GAGG;AACH,wBAAsB,wBAAwB,CAAC,IAAI,EAAE;IACnD,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,GAAG,OAAO,CAAC,mBAAmB,CAAC,CAgB/B"}

package/dist/cli/contradiction-cli.js

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+import { resolve } from 'node:path';
+import { closeDb, openDb } from '../db/client.js';
+import { createLlmProvider } from '../llm/provider.js';
+import { contradictionScan } from './contradiction.js';
+/**
+ * CLI wrapper for the contradiction scan command.
+ * Sets up DB connection and LLM provider, runs the scan, cleans up.
+ */
+export async function contradictionScanCommand(opts) {
+    const wikiPath = resolve(opts.wikiPath ?? '.kg/wiki');
+    const dbPath = opts.dbPath ?? resolve(wikiPath, '..', 'kg.db');
+    const bundle = openDb(dbPath);
+    try {
+        const llmProvider = createLlmProvider();
+        return await contradictionScan({
+            bundle,
+            scope: opts.scope,
+            llmProvider,
+            wikiRoot: wikiPath,
+        });
+    }
+    finally {
+        closeDb(bundle);
+    }
+}
+//# sourceMappingURL=contradiction-cli.js.map

package/dist/cli/contradiction-cli.js.map

@@ -0,0 +1 @@
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package/dist/cli/contradiction.d.ts

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+import type { DbBundle } from '../db/client.js';
+import type { LlmProvider } from '../llm/provider.js';
+/**
+ * Contradiction detector CLI command (PRD Phase 8, stretch goal H).
+ *
+ * Scans wiki chunks for contradictory claims using pairwise LLM judge.
+ * Rate-limited to 1 scan per hour. Outputs contradictions.md to wiki root.
+ */
+export interface ContradictionScanOpts {
+    bundle: DbBundle;
+    scope: 'project' | 'personal';
+    llmProvider: LlmProvider;
+    wikiRoot: string;
+}
+export interface Contradiction {
+    chunkA: {
+        id: string;
+        source_uri: string;
+        text: string;
+    };
+    chunkB: {
+        id: string;
+        source_uri: string;
+        text: string;
+    };
+    explanation: string;
+    confidence: 'high' | 'medium';
+}
+export interface ContradictionResult {
+    scanned_pairs: number;
+    contradictions: Contradiction[];
+    rate_limited: boolean;
+}
+/**
+ * Run a contradiction scan. Returns immediately if rate-limited.
+ */
+export declare function contradictionScan(opts: ContradictionScanOpts): Promise<ContradictionResult>;
+interface ChunkInfo {
+    id: string;
+    source_uri: string;
+    text: string;
+}
+interface CandidatePair {
+    a: ChunkInfo;
+    b: ChunkInfo;
+}
+/**
+ * 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).
+ */
+declare function findCandidatePairs(bundle: DbBundle, scope: string): CandidatePair[];
+declare function parseJudgment(response: string): {
+    contradicts: boolean;
+    explanation: string;
+    confidence: string;
+} | null;
+export { findCandidatePairs as _findCandidatePairs, parseJudgment as _parseJudgment };
+//# sourceMappingURL=contradiction.d.ts.map

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

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+{"version":3,"file":"contradiction.d.ts","sourceRoot":"","sources":["../../src/cli/contradiction.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AAGtD;;;;;GAKG;AAEH,MAAM,WAAW,qBAAqB;IACpC,MAAM,EAAE,QAAQ,CAAC;IACjB,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;IAC9B,WAAW,EAAE,WAAW,CAAC;IACzB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACzD,MAAM,EAAE;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACzD,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,GAAG,QAAQ,CAAC;CAC/B;AAED,MAAM,WAAW,mBAAmB;IAClC,aAAa,EAAE,MAAM,CAAC;IACtB,cAAc,EAAE,aAAa,EAAE,CAAC;IAChC,YAAY,EAAE,OAAO,CAAC;CACvB;AAQD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,qBAAqB,GAC1B,OAAO,CAAC,mBAAmB,CAAC,CAmE9B;AAMD,UAAU,SAAS;IACjB,EAAE,EAAE,MAAM,CAAC;IACX,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,UAAU,aAAa;IACrB,CAAC,EAAE,SAAS,CAAC;IACb,CAAC,EAAE,SAAS,CAAC;CACd;AAED;;;;GAIG;AACH,iBAAS,kBAAkB,CAAC,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,MAAM,GAAG,aAAa,EAAE,CAwD5E;AAED,iBAAS,aAAa,CACpB,QAAQ,EAAE,MAAM,GACf;IAAE,WAAW,EAAE,OAAO,CAAC;IAAC,WAAW,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAkB1E;AAyDD,OAAO,EAAE,kBAAkB,IAAI,mBAAmB,EAAE,aAAa,IAAI,cAAc,EAAE,CAAC"}

package/dist/cli/contradiction.js

@@ -0,0 +1,172 @@
+import { logger } from '../observability/logger.js';
+const RATE_LIMIT_MS = 60 * 60 * 1000; // 1 hour
+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.`;
+/**
+ * Run a contradiction scan. Returns immediately if rate-limited.
+ */
+export async function contradictionScan(opts) {
+    const { bundle, scope, llmProvider, wikiRoot } = opts;
+    // Rate limit check
+    const lastScan = bundle.writer
+        .prepare(`SELECT value FROM kg_meta WHERE key = ?`)
+        .get('last_contradiction_scan');
+    if (lastScan) {
+        const lastTs = parseInt(lastScan.value, 10);
+        if (Date.now() - lastTs < RATE_LIMIT_MS) {
+            return { scanned_pairs: 0, contradictions: [], rate_limited: true };
+        }
+    }
+    if (!llmProvider.available()) {
+        throw new Error('No LLM provider available for contradiction detection. ' +
+            'Set KG_OLLAMA_URL, ANTHROPIC_API_KEY, or OPENAI_API_KEY, ' +
+            'or install the claude/codex CLI.');
+    }
+    // Find candidate pairs via vector similarity
+    const pairs = findCandidatePairs(bundle, scope);
+    const contradictions = [];
+    let scanned = 0;
+    for (const pair of pairs) {
+        try {
+            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,
+            });
+            const judgment = parseJudgment(response);
+            if (judgment && judgment.contradicts && (judgment.confidence === 'high' || judgment.confidence === 'medium')) {
+                contradictions.push({
+                    chunkA: pair.a,
+                    chunkB: pair.b,
+                    explanation: judgment.explanation,
+                    confidence: judgment.confidence,
+                });
+            }
+            scanned++;
+        }
+        catch (err) {
+            logger.warn({ err, pairA: pair.a.id, pairB: pair.b.id }, 'contradiction check failed for pair');
+        }
+    }
+    // Update rate limit timestamp
+    bundle.writer
+        .prepare(`INSERT OR REPLACE INTO kg_meta (key, value) VALUES ('last_contradiction_scan', ?)`)
+        .run(String(Date.now()));
+    // Write contradictions.md if any found
+    if (contradictions.length > 0) {
+        writeContradictionReport(wikiRoot, contradictions, bundle, scope);
+    }
+    return { scanned_pairs: scanned, contradictions, rate_limited: false };
+}
+/**
+ * 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).
+ */
+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 kg_chunks c
+       JOIN kg_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 kg_chunks_vec
+         WHERE embedding MATCH (SELECT embedding FROM kg_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;
+        }
+    }
+    return result;
+}
+function parseJudgment(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',
+        };
+    }
+    catch {
+        return null;
+    }
+}
+function writeContradictionReport(wikiRoot, contradictions, bundle, scope) {
+    const { writeFileSync } = require('node:fs');
+    const { join } = require('node:path');
+    const lines = [
+        '# Detected Contradictions',
+        '',
+        `*Last scanned: ${new Date().toISOString()}*`,
+        '',
+    ];
+    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}`);
+        lines.push('');
+    }
+    writeFileSync(join(wikiRoot, 'contradictions.md'), lines.join('\n'), 'utf8');
+    // Log the scan
+    try {
+        bundle.writer
+            .prepare(`INSERT INTO kg_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 };
+//# sourceMappingURL=contradiction.js.map

package/dist/cli/contradiction.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"contradiction.js","sourceRoot":"","sources":["../../src/cli/contradiction.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,MAAM,EAAE,MAAM,4BAA4B,CAAC;AA6BpD,MAAM,aAAa,GAAG,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC,CAAC,SAAS;AAC/C,MAAM,SAAS,GAAG,EAAE,CAAC;AACrB,MAAM,oBAAoB,GAAG,GAAG,CAAC;AAEjC,MAAM,YAAY,GAAG,0SAA0S,CAAC;AAEhU;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,IAA2B;IAE3B,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;IAEtD,mBAAmB;IACnB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM;SAC3B,OAAO,CACN,yCAAyC,CAC1C;SACA,GAAG,CAAC,yBAAyB,CAAC,CAAC;IAElC,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;QAC5C,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,MAAM,GAAG,aAAa,EAAE,CAAC;YACxC,OAAO,EAAE,aAAa,EAAE,CAAC,EAAE,cAAc,EAAE,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,CAAC;QACtE,CAAC;IACH,CAAC;IAED,IAAI,CAAC,WAAW,CAAC,SAAS,EAAE,EAAE,CAAC;QAC7B,MAAM,IAAI,KAAK,CACb,yDAAyD;YACvD,2DAA2D;YAC3D,kCAAkC,CACrC,CAAC;IACJ,CAAC;IAED,6CAA6C;IAC7C,MAAM,KAAK,GAAG,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEhD,MAAM,cAAc,GAAoB,EAAE,CAAC;IAC3C,IAAI,OAAO,GAAG,CAAC,CAAC;IAEhB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,MAAM,WAAW,CAAC,QAAQ,CAAC;gBAC1C,MAAM,EAAE,YAAY;gBACpB,MAAM,EAAE,iBAAiB,IAAI,CAAC,CAAC,CAAC,UAAU,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,qBAAqB,IAAI,CAAC,CAAC,CAAC,UAAU,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,EAAE;gBACtH,SAAS,EAAE,GAAG;aACf,CAAC,CAAC;YAEH,MAAM,QAAQ,GAAG,aAAa,CAAC,QAAQ,CAAC,CAAC;YACzC,IAAI,QAAQ,IAAI,QAAQ,CAAC,WAAW,IAAI,CAAC,QAAQ,CAAC,UAAU,KAAK,MAAM,IAAI,QAAQ,CAAC,UAAU,KAAK,QAAQ,CAAC,EAAE,CAAC;gBAC7G,cAAc,CAAC,IAAI,CAAC;oBAClB,MAAM,EAAE,IAAI,CAAC,CAAC;oBACd,MAAM,EAAE,IAAI,CAAC,CAAC;oBACd,WAAW,EAAE,QAAQ,CAAC,WAAW;oBACjC,UAAU,EAAE,QAAQ,CAAC,UAAU;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,OAAO,EAAE,CAAC;QACZ,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,qCAAqC,CAAC,CAAC;QAClG,CAAC;IACH,CAAC;IAED,8BAA8B;IAC9B,MAAM,CAAC,MAAM;SACV,OAAO,CACN,mFAAmF,CACpF;SACA,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;IAE3B,uCAAuC;IACvC,IAAI,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9B,wBAAwB,CAAC,QAAQ,EAAE,cAAc,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;IACpE,CAAC;IAED,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,KAAK,EAAE,CAAC;AACzE,CAAC;AAiBD;;;;GAIG;AACH,SAAS,kBAAkB,CAAC,MAAgB,EAAE,KAAa;IACzD,2CAA2C;IAC3C,MAAM,MAAM,GAAG,MAAM,CAAC,MAAM;SACzB,OAAO,CACN;;;;wBAIkB,CACnB;SACA,GAAG,CAAC,KAAK,CAAC,CAAC;IAEd,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IAEjC,sDAAsD;IACtD,MAAM,KAAK,GAAG,IAAI,GAAG,EAAU,CAAC;IAChC,MAAM,MAAM,GAAoB,EAAE,CAAC;IAEnC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,MAAM,IAAI,SAAS;YAAE,MAAM;QAEtC,MAAM,OAAO,GAAG,MAAM,CAAC,MAAM;aAC1B,OAAO,CACN;;;;2BAImB,CACpB;aACA,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,iCAAiC;QAEzD,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE,CAAC;YAC1B,IAAI,GAAG,CAAC,KAAK,KAAK,KAAK,CAAC,KAAK;gBAAE,SAAS;YACxC,IAAI,GAAG,CAAC,QAAQ,GAAG,oBAAoB;gBAAE,SAAS;YAElD,8BAA8B;YAC9B,MAAM,OAAO,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC1D,IAAI,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC;gBAAE,SAAS;YACjC,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;YAEnB,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;YACxD,IAAI,CAAC,KAAK;gBAAE,SAAS;YAErB,iEAAiE;YACjE,IAAI,KAAK,CAAC,UAAU,KAAK,KAAK,CAAC,UAAU;gBAAE,SAAS;YAEpD,MAAM,CAAC,IAAI,CAAC;gBACV,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE;gBACnE,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE;aACpE,CAAC,CAAC;YAEH,IAAI,MAAM,CAAC,MAAM,IAAI,SAAS;gBAAE,MAAM;QACxC,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,aAAa,CACpB,QAAgB;IAEhB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC;QAC5C,IAAI,CAAC,KAAK;YAAE,OAAO,IAAI,CAAC;QACxB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAIjC,CAAC;QACF,IAAI,OAAO,MAAM,CAAC,WAAW,KAAK,SAAS;YAAE,OAAO,IAAI,CAAC;QACzD,OAAO;YACL,WAAW,EAAE,MAAM,CAAC,WAAW;YAC/B,WAAW,EAAE,MAAM,CAAC,WAAW,IAAI,EAAE;YACrC,UAAU,EAAE,MAAM,CAAC,UAAU,IAAI,KAAK;SACvC,CAAC;IACJ,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,SAAS,wBAAwB,CAC/B,QAAgB,EAChB,cAA+B,EAC/B,MAAgB,EAChB,KAAa;IAEb,MAAM,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC,SAAS,CAA6B,CAAC;IACzE,MAAM,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC,WAAW,CAA+B,CAAC;IAEpE,MAAM,KAAK,GAAG;QACZ,2BAA2B;QAC3B,EAAE;QACF,kBAAkB,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,GAAG;QAC7C,EAAE;KACH,CAAC;IAEF,KAAK,MAAM,CAAC,IAAI,cAAc,EAAE,CAAC;QAC/B,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,UAAU,OAAO,CAAC,CAAC,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAClE,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CACR,kBAAkB,CAAC,CAAC,MAAM,CAAC,UAAU,OAAO,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,GAAG,CAC5E,CAAC;QACF,KAAK,CAAC,IAAI,CACR,kBAAkB,CAAC,CAAC,MAAM,CAAC,UAAU,OAAO,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,GAAG,CAC5E,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;QAClD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package/dist/cli/index.js

@@ -1,5 +1,6 @@
 #!/usr/bin/env node
 import { auditCommand, renderAudit } from './audit.js';
+import { contradictionScanCommand } from './contradiction-cli.js';
 import { exportCommand, renderExport } from './export.js';
 import { importCommand, renderImport } from './import.js';
 import { purgeCommand, renderPurge } from './purge.js';
@@ -143,6 +144,27 @@ async function main() {
             console.log(renderImport(result));
             break;
         }
+        case 'contradiction-scan': {
+            const scope = (getString(flags, 'scope') ?? 'project');
+            const result = await contradictionScanCommand({
+                scope,
+                wikiPath: getString(flags, 'wiki-path'),
+                dbPath: getString(flags, 'db-path'),
+            });
+            if (result.rate_limited) {
+                // eslint-disable-next-line no-console
+                console.log('Rate limited — last scan was less than 1 hour ago.');
+            }
+            else {
+                // eslint-disable-next-line no-console
+                console.log(`Scanned ${result.scanned_pairs} pairs, found ${result.contradictions.length} contradictions.`);
+                if (result.contradictions.length > 0) {
+                    // eslint-disable-next-line no-console
+                    console.log('Wrote contradictions.md to wiki root.');
+                }
+            }
+            break;
+        }
         case undefined:
         case 'help':
         case '-h':
@@ -157,7 +179,8 @@ Usage:
   kg audit   [--tail] [--n <count>] [--scope project|personal] [--db-path <path>]
   kg purge   --scope <project|personal> --confirm [--db-path <path>]
   kg export  --scope <project|personal> [--out file.json] [--db-path <path>]
-  kg import  --scope <project|personal> --in file.json [--db-path <path>]`);
+  kg import  --scope <project|personal> --in file.json [--db-path <path>]
+  kg contradiction-scan [--scope project|personal] [--wiki-path <dir>] [--db-path <path>]`);
             break;
         }
         default:

package/dist/cli/index.js.map

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package/dist/cli/rebuild.js

@@ -52,6 +52,22 @@ async function rebuildOneScope(args) {
     const t0 = Date.now();
     const bundle = openDb(dbPath);
     try {
+        // Clean up legacy absolute file:// URIs before rebuild (0.1.9+ migration).
+        if (scope === 'project') {
+            try {
+                const orphaned = bundle.writer
+                    .prepare("SELECT COUNT(*) AS cnt FROM kg_nodes WHERE scope = 'project' AND source_uri LIKE 'file://%'")
+                    .get();
+                if (orphaned.cnt > 0) {
+                    logger.info({ count: orphaned.cnt }, 'rebuild: deleting legacy absolute-path rows');
+                    bundle.writer.exec("DELETE FROM kg_chunks_vec WHERE rowid IN (SELECT c.rowid FROM kg_chunks c JOIN kg_nodes n ON c.node_id = n.id WHERE n.scope = 'project' AND n.source_uri LIKE 'file://%')");
+                    bundle.writer.exec("DELETE FROM kg_nodes WHERE scope = 'project' AND source_uri LIKE 'file://%'");
+                }
+            }
+            catch (err) {
+                logger.warn({ err }, 'legacy URI cleanup failed — continuing');
+            }
+        }
         const ingester = new IngesterService(bundle, embedder, scope, wikiDir);
         const files = listMarkdownFiles(wikiDir);
         let nodes = 0;

package/dist/cli/rebuild.js.map

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

@@ -183,6 +183,25 @@ function makeOnEvent(ingester) {
     };
 }
 async function runStartupConsistency(ingester, wikiDir, scope, writer) {
+    // Migrate legacy absolute file:// URIs to relative paths (0.1.9+).
+    // Old project-scope rows have source_uri like "file:///abs/path/auth.md";
+    // new rows use relative paths like "auth.md". Delete the orphans so they
+    // don't pollute search results after re-ingest.
+    if (scope === 'project' && writer) {
+        try {
+            const orphaned = writer
+                .prepare("SELECT COUNT(*) AS cnt FROM kg_nodes WHERE scope = 'project' AND source_uri LIKE 'file://%'")
+                .get();
+            if (orphaned.cnt > 0) {
+                logger.info({ count: orphaned.cnt }, 'migrating legacy absolute-path rows — deleting orphans before re-ingest');
+                writer.exec("DELETE FROM kg_chunks_vec WHERE rowid IN (SELECT c.rowid FROM kg_chunks c JOIN kg_nodes n ON c.node_id = n.id WHERE n.scope = 'project' AND n.source_uri LIKE 'file://%')");
+                writer.exec("DELETE FROM kg_nodes WHERE scope = 'project' AND source_uri LIKE 'file://%'");
+            }
+        }
+        catch (err) {
+            logger.warn({ err }, 'legacy URI migration check failed — continuing');
+        }
+    }
     ingester.reloadManifest();
     const manifest = ingester.getManifest();
     const stale = checkConsistency(manifest, wikiDir, scope, writer);

package/dist/cli/serve.js.map

@@ -1 +1 @@
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package/dist/ingest/ingester.d.ts

@@ -112,6 +112,11 @@ export declare class IngesterService {
  * caller passes `--clean` to force a full re-ingest from scratch.
  */
 export declare function freshManifest(): Manifest;
+/**
+ * Extract wikilink targets from markdown content.
+ * Returns deduplicated, normalized (trimmed, lowercase) link targets.
+ */
+export declare function extractWikilinks(content: string): string[];
 export type { ChunkText };
 export { manifestPathFor };
 export { fileSha };

package/dist/ingest/ingester.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ingester.d.ts","sourceRoot":"","sources":["../../src/ingest/ingester.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AAGzD,OAAO,EACL,KAAK,QAAQ,EAGb,OAAO,EACP,eAAe,EAOhB,MAAM,eAAe,CAAC;AAGvB,OAAO,EAAgB,KAAK,KAAK,IAAI,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAEzE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyCG;AAMH,MAAM,MAAM,KAAK,GAAG,SAAS,GAAG,UAAU,CAAC;AAE3C,MAAM,WAAW,YAAY;IAC3B,+CAA+C;IAC/C,YAAY,EAAE,MAAM,CAAC;IACrB,oEAAoE;IACpE,cAAc,EAAE,MAAM,CAAC;IACvB,qDAAqD;IACrD,cAAc,EAAE,MAAM,CAAC;IACvB,uDAAuD;IACvD,aAAa,EAAE,MAAM,CAAC;IACtB,oFAAoF;IACpF,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,eAAe;IAC9B,oFAAoF;IACpF,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAoBD,gFAAgF;AAChF,wBAAgB,2BAA2B,IAAI,IAAI,CAElD;AAMD,qBAAa,eAAe;IAMxB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,QAAQ;IACzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IAPxB,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAS;gBAGf,MAAM,EAAE,QAAQ,EAChB,QAAQ,EAAE,QAAQ,EAClB,KAAK,EAAE,KAAK,EAC7B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,eAAoB;IAO/B;;;;;;OAMG;IACG,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC;IAsBxD;;;;OAIG;IACH,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI;IAcjC;;;OAGG;IACH,WAAW,IAAI,QAAQ;IAIvB;;;OAGG;IACH,cAAc,IAAI,IAAI;YAQR,cAAc;IAkM5B;;;;;;OAMG;IACH,OAAO,CAAC,sBAAsB;IA4B9B,OAAO,CAAC,gBAAgB;IAKxB,OAAO,CAAC,SAAS;CAYlB;AAsCD;;;GAGG;AACH,wBAAgB,aAAa,IAAI,QAAQ,CAExC;AAGD,YAAY,EAAE,SAAS,EAAE,CAAC;AAC1B,OAAO,EAAE,eAAe,EAAE,CAAC;AAC3B,OAAO,EAAE,OAAO,EAAE,CAAC"}
+{"version":3,"file":"ingester.d.ts","sourceRoot":"","sources":["../../src/ingest/ingester.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AAGzD,OAAO,EACL,KAAK,QAAQ,EAGb,OAAO,EACP,eAAe,EAOhB,MAAM,eAAe,CAAC;AAGvB,OAAO,EAAgB,KAAK,KAAK,IAAI,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAEzE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyCG;AAMH,MAAM,MAAM,KAAK,GAAG,SAAS,GAAG,UAAU,CAAC;AAE3C,MAAM,WAAW,YAAY;IAC3B,+CAA+C;IAC/C,YAAY,EAAE,MAAM,CAAC;IACrB,oEAAoE;IACpE,cAAc,EAAE,MAAM,CAAC;IACvB,qDAAqD;IACrD,cAAc,EAAE,MAAM,CAAC;IACvB,uDAAuD;IACvD,aAAa,EAAE,MAAM,CAAC;IACtB,oFAAoF;IACpF,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,eAAe;IAC9B,oFAAoF;IACpF,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAoBD,gFAAgF;AAChF,wBAAgB,2BAA2B,IAAI,IAAI,CAElD;AAMD,qBAAa,eAAe;IAMxB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,QAAQ;IACzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IAPxB,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAS;gBAGf,MAAM,EAAE,QAAQ,EAChB,QAAQ,EAAE,QAAQ,EAClB,KAAK,EAAE,KAAK,EAC7B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,eAAoB;IAO/B;;;;;;OAMG;IACG,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC;IAsBxD;;;;OAIG;IACH,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI;IAcjC;;;OAGG;IACH,WAAW,IAAI,QAAQ;IAIvB;;;OAGG;IACH,cAAc,IAAI,IAAI;YAQR,cAAc;IAmO5B;;;;;;OAMG;IACH,OAAO,CAAC,sBAAsB;IA4B9B,OAAO,CAAC,gBAAgB;IAKxB,OAAO,CAAC,SAAS;CAYlB;AAsCD;;;GAGG;AACH,wBAAgB,aAAa,IAAI,QAAQ,CAExC;AASD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE,CAO1D;AAiCD,YAAY,EAAE,SAAS,EAAE,CAAC;AAC1B,OAAO,EAAE,eAAe,EAAE,CAAC;AAC3B,OAAO,EAAE,OAAO,EAAE,CAAC"}

package/dist/ingest/ingester.js

@@ -166,7 +166,7 @@ export class IngesterService {
                 }
             }
         }
-        // Step 6: transaction — delete-then-insert nodes/chunks/vec for this file
+        // Step 6: transaction — delete-then-insert nodes/chunks/vec/edges for this file
         const now = Date.now();
         const totalChunks = planned.reduce((acc, n) => acc + n.chunks.length, 0);
         this.runInTransaction((w) => {
@@ -183,6 +183,17 @@ export class IngesterService {
                 w.prepare(`DELETE FROM kg_chunks_vec WHERE rowid IN (${placeholders})`).run(...oldRowids.map((r) => r.rowid));
             }
             // Delete old nodes for this file (cascades to chunks → FTS5 trigger fires).
+            // Also delete outbound edges from this file's nodes (edges don't cascade
+            // from kg_nodes FK — they reference src_id/dst_id without ON DELETE CASCADE
+            // on dst_id, so we delete src edges explicitly).
+            const oldNodeIds = w
+                .prepare(`SELECT id FROM kg_nodes WHERE scope = ? AND source_uri = ?`)
+                .all(this.scope, sourceUri)
+                .map((r) => r.id);
+            if (oldNodeIds.length > 0) {
+                const ph = oldNodeIds.map(() => '?').join(',');
+                w.prepare(`DELETE FROM kg_edges WHERE src_id IN (${ph})`).run(...oldNodeIds);
+            }
             w.prepare('DELETE FROM kg_nodes WHERE scope = ? AND source_uri = ?').run(this.scope, sourceUri);
             // Insert new nodes
             const insertNode = w.prepare(`INSERT INTO kg_nodes (id, scope, source_uri, section_path, kind, title, content, source_sha, token_count, created_at, updated_at, last_accessed_at, confidence)
@@ -211,6 +222,20 @@ export class IngesterService {
                     }
                 }
             }
+            // Step 6.5: wikilink edge extraction (D39)
+            // Scan each node's content for [[wikilinks]], resolve targets to
+            // existing node IDs, and insert edges. Unresolved links are silently
+            // skipped (gap detector already surfaces those).
+            const insertEdge = w.prepare(`INSERT OR IGNORE INTO kg_edges (src_id, dst_id, edge_kind) VALUES (?, ?, 'wikilink')`);
+            for (const node of planned) {
+                const links = extractWikilinks(node.section.content);
+                for (const linkTarget of links) {
+                    const dstId = resolveWikilinkTarget(w, this.scope, linkTarget);
+                    if (dstId && dstId !== node.nodeId) {
+                        insertEdge.run(node.nodeId, dstId);
+                    }
+                }
+            }
         });
         // Step 7: append kg_log row
         this.appendLog('ingest:done', absPath, {
@@ -309,6 +334,46 @@ function sha1(input) {
 export function freshManifest() {
     return emptyManifest();
 }
+// ----------------------------------------------------------------------------
+// Wikilink extraction + resolution (D39)
+// ----------------------------------------------------------------------------
+/** Wikilink regex: [[term]] or [[term|display]] — reuses pattern from gaps/detector.ts */
+const WIKILINK_RE = /\[\[([^\]|]+)(?:\|[^\]]+)?\]\]/g;
+/**
+ * Extract wikilink targets from markdown content.
+ * Returns deduplicated, normalized (trimmed, lowercase) link targets.
+ */
+export function extractWikilinks(content) {
+    const targets = new Set();
+    for (const m of content.matchAll(WIKILINK_RE)) {
+        const target = (m[1] ?? '').trim().toLowerCase();
+        if (target.length >= 1)
+            targets.add(target);
+    }
+    return [...targets];
+}
+/**
+ * Resolve a wikilink target string to a node ID. Checks:
+ * 1. source_uri basename match (e.g. "auth" → "auth.md")
+ * 2. title match (case-insensitive)
+ *
+ * Returns the first matching node ID, or null if unresolved.
+ */
+function resolveWikilinkTarget(w, scope, target) {
+    // Try source_uri basename match: "auth" should match "auth.md" or "guides/auth.md"
+    // We match the last path component without .md extension.
+    const withMd = target.endsWith('.md') ? target : `${target}.md`;
+    const row = w
+        .prepare(`SELECT id FROM kg_nodes
+       WHERE scope = ? AND (
+         source_uri = ? OR
+         source_uri LIKE ? OR
+         LOWER(title) = ?
+       )
+       LIMIT 1`)
+        .get(scope, withMd, `%/${withMd}`, target);
+    return row?.id ?? null;
+}
 export { manifestPathFor };
 export { fileSha };
 //# sourceMappingURL=ingester.js.map