@gzoo/cortex 0.5.11 → 0.5.13

package/packages/graph/dist/query-engine.js

@@ -4,6 +4,17 @@ const AVG_CHARS_PER_TOKEN = 4;
 function estimateTokens(text) {
     return Math.ceil(text.length / AVG_CHARS_PER_TOKEN);
 }
+const FTS_STOP_WORDS = new Set([
+    'a', 'an', 'the', 'and', 'or', 'but', 'in', 'on', 'at', 'to', 'for',
+    'of', 'with', 'by', 'from', 'is', 'are', 'was', 'were', 'be', 'been',
+    'being', 'have', 'has', 'had', 'do', 'does', 'did', 'will', 'would',
+    'could', 'should', 'may', 'might', 'shall', 'can', 'need', 'must',
+    'what', 'which', 'who', 'how', 'why', 'when', 'where', 'that', 'this',
+    'these', 'those', 'it', 'its', 'me', 'my', 'you', 'your', 'we', 'our',
+    'they', 'their', 'he', 'she', 'i', 'all', 'any', 'each', 'some', 'no',
+    'not', 'so', 'yet', 'use', 'used', 'using', 'about', 'tell', 'know',
+    'get', 'got', 'make', 'made', 'see', 'give', 'go', 'come', 'take',
+]);
 export class QueryEngine {
     sqliteStore;
     vectorStore;
@@ -42,19 +53,10 @@ export class QueryEngine {
         }
         // Filter entities by project privacy level
         const privacyFiltered = await this.filterByPrivacy(contextEntities);
-        // Gather relationships between context entities
+        // Gather relationships between context entities (single batch query)
         const entityIds = new Set(privacyFiltered.map((e) => e.id));
-        const relationships = [];
-        for (const entity of privacyFiltered) {
-            const rels = await this.sqliteStore.getRelationshipsForEntity(entity.id);
-            for (const rel of rels) {
-                if (entityIds.has(rel.sourceEntityId) && entityIds.has(rel.targetEntityId)) {
-                    relationships.push(rel);
-                }
-            }
-        }
-        // Deduplicate relationships
-        const uniqueRels = [...new Map(relationships.map((r) => [r.id, r])).values()];
+        const allRels = await this.sqliteStore.getRelationshipsForEntities([...entityIds]);
+        const uniqueRels = allRels.filter((r) => entityIds.has(r.sourceEntityId) && entityIds.has(r.targetEntityId));
         const relTokens = uniqueRels.reduce((sum, r) => sum + estimateTokens(r.description ?? '') + 20, 0);
         // Recalculate tokens after privacy filtering (content may have been redacted)
         const filteredTokens = privacyFiltered.reduce((sum, e) => sum + estimateTokens(e.content) + estimateTokens(e.name), 0);
@@ -110,22 +112,11 @@ export class QueryEngine {
      * entities matching ANY meaningful keyword are returned.
      */
     buildFtsQuery(query) {
-        const stopWords = new Set([
-            'a', 'an', 'the', 'and', 'or', 'but', 'in', 'on', 'at', 'to', 'for',
-            'of', 'with', 'by', 'from', 'is', 'are', 'was', 'were', 'be', 'been',
-            'being', 'have', 'has', 'had', 'do', 'does', 'did', 'will', 'would',
-            'could', 'should', 'may', 'might', 'shall', 'can', 'need', 'must',
-            'what', 'which', 'who', 'how', 'why', 'when', 'where', 'that', 'this',
-            'these', 'those', 'it', 'its', 'me', 'my', 'you', 'your', 'we', 'our',
-            'they', 'their', 'he', 'she', 'i', 'all', 'any', 'each', 'some', 'no',
-            'not', 'so', 'yet', 'use', 'used', 'using', 'about', 'tell', 'know',
-            'get', 'got', 'make', 'made', 'see', 'give', 'go', 'come', 'take',
-        ]);
         const keywords = query
-            .replace(/[^a-zA-Z0-9\s]/g, ' ') // strip all non-alphanumeric chars (catches ?, !, ., etc.)
+            .replace(/[^a-zA-Z0-9\s]/g, ' ')
             .toLowerCase()
             .split(/\s+/)
-            .filter((w) => w.length >= 3 && !stopWords.has(w));
+            .filter((w) => w.length >= 3 && !FTS_STOP_WORDS.has(w));
         if (keywords.length === 0) {
             // Fallback: sanitize raw query for FTS5 safety
             return query.replace(/[^a-zA-Z0-9\s]/g, ' ').trim();

package/packages/graph/dist/query-engine.js.map

@@ -1 +1 @@
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package/packages/graph/dist/sqlite-store.d.ts

@@ -60,14 +60,18 @@ export declare class SQLiteStore implements GraphStore {
     private migrate;
     private backupSync;
     close(): void;
+    transaction<T>(fn: () => T): T;
+    createEntitySync(entity: Omit<Entity, 'id' | 'createdAt' | 'updatedAt'>): Entity;
     createEntity(entity: Omit<Entity, 'id' | 'createdAt' | 'updatedAt'>): Promise<Entity>;
+    private _createEntity;
     getEntity(id: string): Promise<Entity | null>;
     updateEntity(id: string, updates: Partial<Entity>): Promise<Entity>;
     deleteEntity(id: string, soft?: boolean): Promise<void>;
     findEntities(query: EntityQuery): Promise<Entity[]>;
     createRelationship(rel: Omit<Relationship, 'id' | 'createdAt' | 'updatedAt'>): Promise<Relationship>;
     getRelationship(id: string): Promise<Relationship | null>;
-    getRelationshipsForEntity(entityId: string, direction?: 'in' | 'out' | 'both'): Promise<Relationship[]>;
+    getRelationshipsForEntity(entityId: string, direction?: 'in' | 'out' | 'both', limit?: number): Promise<Relationship[]>;
+    getRelationshipsForEntities(entityIds: string[]): Promise<Relationship[]>;
     deleteRelationship(id: string): Promise<void>;
     deleteBySourcePath(pathPrefix: string): {
         deletedEntities: number;

package/packages/graph/dist/sqlite-store.d.ts.map

@@ -1 +1 @@
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package/packages/graph/dist/sqlite-store.js

@@ -5,6 +5,7 @@ import { dirname } from 'node:path';
 import { homedir } from 'node:os';
 import { CortexError, GRAPH_DB_ERROR, GRAPH_ENTITY_NOT_FOUND, } from '@cortex/core';
 import { up as applyInitialMigration } from './migrations/001-initial.js';
+import { up as applyIndexMigration } from './migrations/002-add-indexes.js';
 function resolveHomePath(p) {
     return p.startsWith('~') ? p.replace('~', homedir()) : p;
 }
@@ -93,11 +94,16 @@ export class SQLiteStore {
     constructor(options = {}) {
         const { dbPath = '~/.cortex/cortex.db', walMode = true, backupOnStartup = true, } = options;
         this.dbPath = resolveHomePath(dbPath);
-        mkdirSync(dirname(this.dbPath), { recursive: true });
+        mkdirSync(dirname(this.dbPath), { recursive: true, mode: 0o700 });
         if (backupOnStartup) {
             this.backupSync();
         }
         this.db = new Database(this.dbPath);
+        // Restrict DB file permissions (owner-only read/write)
+        try {
+            chmodSync(this.dbPath, 0o600);
+        }
+        catch { /* Windows — ignore */ }
         if (walMode) {
             this.db.pragma('journal_mode = WAL');
         }
@@ -108,6 +114,7 @@ export class SQLiteStore {
     migrate() {
         try {
             applyInitialMigration(this.db);
+            applyIndexMigration(this.db);
         }
         catch (err) {
             throw new CortexError(GRAPH_DB_ERROR, 'critical', 'graph', `Migration failed: ${err instanceof Error ? err.message : String(err)}`, undefined, 'Delete the database and restart.');
@@ -132,28 +139,37 @@ export class SQLiteStore {
     close() {
         this.db.close();
     }
+    transaction(fn) {
+        return this.db.transaction(fn)();
+    }
     // --- Entities ---
+    createEntitySync(entity) {
+        return this._createEntity(entity);
+    }
     async createEntity(entity) {
+        return this._createEntity(entity);
+    }
+    _createEntity(entity) {
         const id = randomUUID();
         const ts = now();
-        this.db.prepare(`
-      INSERT INTO entities (
-        id, type, name, content, summary, properties, confidence,
-        source_file, source_start_line, source_end_line,
-        project_id, extracted_by, tags, status, created_at, updated_at
-      ) VALUES (
-        ?, ?, ?, ?, ?, ?, ?,
-        ?, ?, ?,
-        ?, ?, ?, ?, ?, ?
-      )
+        this.db.prepare(`
+      INSERT INTO entities (
+        id, type, name, content, summary, properties, confidence,
+        source_file, source_start_line, source_end_line,
+        project_id, extracted_by, tags, status, created_at, updated_at
+      ) VALUES (
+        ?, ?, ?, ?, ?, ?, ?,
+        ?, ?, ?,
+        ?, ?, ?, ?, ?, ?
+      )
     `).run(id, entity.type, entity.name, entity.content, entity.summary ?? null, JSON.stringify(entity.properties), entity.confidence, entity.sourceFile, entity.sourceRange?.startLine ?? null, entity.sourceRange?.endLine ?? null, entity.projectId, JSON.stringify(entity.extractedBy), JSON.stringify(entity.tags), entity.status, ts, ts);
         // Sync to FTS
-        this.db.prepare(`
-      INSERT INTO entities_fts (rowid, name, content, summary, tags)
-      VALUES (
-        (SELECT rowid FROM entities WHERE id = ?),
-        ?, ?, ?, ?
-      )
+        this.db.prepare(`
+      INSERT INTO entities_fts (rowid, name, content, summary, tags)
+      VALUES (
+        (SELECT rowid FROM entities WHERE id = ?),
+        ?, ?, ?, ?
+      )
     `).run(id, entity.name, entity.content, entity.summary ?? '', entity.tags.join(' '));
         return { ...entity, id, createdAt: ts, updatedAt: ts };
     }
@@ -167,18 +183,18 @@ export class SQLiteStore {
             throw new CortexError(GRAPH_ENTITY_NOT_FOUND, 'low', 'graph', `Entity not found: ${id}`, { entityId: id });
         }
         const merged = { ...existing, ...updates, updatedAt: now() };
-        this.db.prepare(`
-      UPDATE entities SET
-        type = ?, name = ?, content = ?, summary = ?,
-        properties = ?, confidence = ?,
-        source_file = ?, source_start_line = ?, source_end_line = ?,
-        extracted_by = ?, tags = ?, status = ?, updated_at = ?
-      WHERE id = ?
+        this.db.prepare(`
+      UPDATE entities SET
+        type = ?, name = ?, content = ?, summary = ?,
+        properties = ?, confidence = ?,
+        source_file = ?, source_start_line = ?, source_end_line = ?,
+        extracted_by = ?, tags = ?, status = ?, updated_at = ?
+      WHERE id = ?
     `).run(merged.type, merged.name, merged.content, merged.summary ?? null, JSON.stringify(merged.properties), merged.confidence, merged.sourceFile, merged.sourceRange?.startLine ?? null, merged.sourceRange?.endLine ?? null, JSON.stringify(merged.extractedBy), JSON.stringify(merged.tags), merged.status, merged.updatedAt, id);
         // Re-sync FTS
-        this.db.prepare(`
-      UPDATE entities_fts SET name = ?, content = ?, summary = ?, tags = ?
-      WHERE rowid = (SELECT rowid FROM entities WHERE id = ?)
+        this.db.prepare(`
+      UPDATE entities_fts SET name = ?, content = ?, summary = ?, tags = ?
+      WHERE rowid = (SELECT rowid FROM entities WHERE id = ?)
     `).run(merged.name, merged.content, merged.summary ?? '', merged.tags.join(' '), id);
         return merged;
     }
@@ -217,20 +233,25 @@ export class SQLiteStore {
         }
         let sql;
         if (query.search) {
+            // Sanitize FTS input: strip operators to prevent FTS5 injection
+            const sanitizedSearch = query.search.replace(/[^a-zA-Z0-9\s]/g, ' ').trim();
+            if (!sanitizedSearch) {
+                return [];
+            }
             // Use FTS for text search
-            sql = `
-        SELECT e.* FROM entities e
-        JOIN entities_fts fts ON fts.rowid = e.rowid
-        WHERE fts.entities_fts MATCH ? AND ${conditions.join(' AND ')}
-        ORDER BY rank
+            sql = `
+        SELECT e.* FROM entities e
+        JOIN entities_fts fts ON fts.rowid = e.rowid
+        WHERE fts.entities_fts MATCH ? AND ${conditions.join(' AND ')}
+        ORDER BY rank
       `;
-            params.unshift(query.search);
+            params.unshift(sanitizedSearch);
         }
         else {
-            sql = `
-        SELECT * FROM entities
-        WHERE ${conditions.join(' AND ')}
-        ORDER BY created_at DESC
+            sql = `
+        SELECT * FROM entities
+        WHERE ${conditions.join(' AND ')}
+        ORDER BY created_at DESC
       `;
         }
         if (query.limit) {
@@ -248,12 +269,12 @@ export class SQLiteStore {
     async createRelationship(rel) {
         const id = randomUUID();
         const ts = now();
-        this.db.prepare(`
-      INSERT INTO relationships (
-        id, type, source_entity_id, target_entity_id,
-        description, confidence, properties, extracted_by,
-        created_at, updated_at
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        this.db.prepare(`
+      INSERT INTO relationships (
+        id, type, source_entity_id, target_entity_id,
+        description, confidence, properties, extracted_by,
+        created_at, updated_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
     `).run(id, rel.type, rel.sourceEntityId, rel.targetEntityId, rel.description ?? null, rel.confidence, JSON.stringify(rel.properties), JSON.stringify(rel.extractedBy), ts, ts);
         return { ...rel, id, createdAt: ts, updatedAt: ts };
     }
@@ -261,24 +282,37 @@ export class SQLiteStore {
         const row = this.db.prepare('SELECT * FROM relationships WHERE id = ?').get(id);
         return row ? rowToRelationship(row) : null;
     }
-    async getRelationshipsForEntity(entityId, direction = 'both') {
+    async getRelationshipsForEntity(entityId, direction = 'both', limit = 200) {
         let sql;
         let params;
         if (direction === 'out') {
-            sql = 'SELECT * FROM relationships WHERE source_entity_id = ?';
-            params = [entityId];
+            sql = 'SELECT * FROM relationships WHERE source_entity_id = ? LIMIT ?';
+            params = [entityId, limit];
         }
         else if (direction === 'in') {
-            sql = 'SELECT * FROM relationships WHERE target_entity_id = ?';
-            params = [entityId];
+            sql = 'SELECT * FROM relationships WHERE target_entity_id = ? LIMIT ?';
+            params = [entityId, limit];
         }
         else {
-            sql = 'SELECT * FROM relationships WHERE source_entity_id = ? OR target_entity_id = ?';
-            params = [entityId, entityId];
+            sql = 'SELECT * FROM relationships WHERE source_entity_id = ? OR target_entity_id = ? LIMIT ?';
+            params = [entityId, entityId, limit];
         }
         const rows = this.db.prepare(sql).all(...params);
         return rows.map(rowToRelationship);
     }
+    async getRelationshipsForEntities(entityIds) {
+        if (entityIds.length === 0)
+            return [];
+        const placeholders = entityIds.map(() => '?').join(',');
+        const sql = `
+      SELECT * FROM relationships
+      WHERE source_entity_id IN (${placeholders})
+         OR target_entity_id IN (${placeholders})
+      LIMIT 2000
+    `;
+        const rows = this.db.prepare(sql).all(...entityIds, ...entityIds);
+        return rows.map(rowToRelationship);
+    }
     async deleteRelationship(id) {
         this.db.prepare('DELETE FROM relationships WHERE id = ?').run(id);
     }
@@ -288,14 +322,14 @@ export class SQLiteStore {
         const escaped = normalized.replace(/[%_\\]/g, '\\$&');
         const pattern = escaped + '%';
         return this.db.transaction(() => {
-            const relResult = this.db.prepare(`
-        DELETE FROM relationships
-        WHERE source_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
-           OR target_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
+            const relResult = this.db.prepare(`
+        DELETE FROM relationships
+        WHERE source_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
+           OR target_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
       `).run(pattern, pattern);
-            this.db.prepare(`
-        DELETE FROM entities_fts
-        WHERE rowid IN (SELECT rowid FROM entities WHERE source_file LIKE ? ESCAPE '\\' AND deleted_at IS NULL)
+            this.db.prepare(`
+        DELETE FROM entities_fts
+        WHERE rowid IN (SELECT rowid FROM entities WHERE source_file LIKE ? ESCAPE '\\' AND deleted_at IS NULL)
       `).run(pattern);
             const entityResult = this.db.prepare("DELETE FROM entities WHERE source_file LIKE ? ESCAPE '\\'").run(pattern);
             const fileResult = this.db.prepare("DELETE FROM files WHERE path LIKE ? ESCAPE '\\'").run(pattern);
@@ -317,14 +351,14 @@ export class SQLiteStore {
     }
     pruneSoftDeleted() {
         return this.db.transaction(() => {
-            const relResult = this.db.prepare(`
-        DELETE FROM relationships
-        WHERE source_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
-           OR target_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
+            const relResult = this.db.prepare(`
+        DELETE FROM relationships
+        WHERE source_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
+           OR target_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
       `).run();
-            this.db.prepare(`
-        DELETE FROM entities_fts
-        WHERE rowid IN (SELECT rowid FROM entities WHERE deleted_at IS NOT NULL)
+            this.db.prepare(`
+        DELETE FROM entities_fts
+        WHERE rowid IN (SELECT rowid FROM entities WHERE deleted_at IS NOT NULL)
       `).run();
             const entityResult = this.db.prepare('DELETE FROM entities WHERE deleted_at IS NOT NULL').run();
             return {
@@ -337,22 +371,22 @@ export class SQLiteStore {
     async upsertFile(file) {
         const existing = this.db.prepare('SELECT * FROM files WHERE path = ?').get(file.path);
         if (existing) {
-            this.db.prepare(`
-        UPDATE files SET
-          relative_path = ?, project_id = ?, content_hash = ?,
-          file_type = ?, size_bytes = ?, last_modified = ?,
-          last_ingested_at = ?, entity_ids = ?, status = ?, parse_error = ?
-        WHERE path = ?
+            this.db.prepare(`
+        UPDATE files SET
+          relative_path = ?, project_id = ?, content_hash = ?,
+          file_type = ?, size_bytes = ?, last_modified = ?,
+          last_ingested_at = ?, entity_ids = ?, status = ?, parse_error = ?
+        WHERE path = ?
       `).run(file.relativePath, file.projectId, file.contentHash, file.fileType, file.sizeBytes, file.lastModified, file.lastIngestedAt ?? null, JSON.stringify(file.entityIds), file.status, file.parseError ?? null, file.path);
             return { ...file, id: existing.id };
         }
         const id = randomUUID();
-        this.db.prepare(`
-      INSERT INTO files (
-        id, path, relative_path, project_id, content_hash,
-        file_type, size_bytes, last_modified, last_ingested_at,
-        entity_ids, status, parse_error
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        this.db.prepare(`
+      INSERT INTO files (
+        id, path, relative_path, project_id, content_hash,
+        file_type, size_bytes, last_modified, last_ingested_at,
+        entity_ids, status, parse_error
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
     `).run(id, file.path, file.relativePath, file.projectId, file.contentHash, file.fileType, file.sizeBytes, file.lastModified, file.lastIngestedAt ?? null, JSON.stringify(file.entityIds), file.status, file.parseError ?? null);
         return { ...file, id };
     }
@@ -368,11 +402,11 @@ export class SQLiteStore {
     async createProject(project) {
         const id = randomUUID();
         const ts = now();
-        this.db.prepare(`
-      INSERT INTO projects (
-        id, name, root_path, privacy_level,
-        file_count, entity_count, last_ingested_at, created_at
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+        this.db.prepare(`
+      INSERT INTO projects (
+        id, name, root_path, privacy_level,
+        file_count, entity_count, last_ingested_at, created_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
     `).run(id, project.name, project.rootPath, project.privacyLevel, project.fileCount, project.entityCount, project.lastIngestedAt ?? null, ts);
         return { ...project, id, createdAt: ts };
     }
@@ -387,11 +421,11 @@ export class SQLiteStore {
     // --- Contradictions ---
     async createContradiction(contradiction) {
         const id = randomUUID();
-        this.db.prepare(`
-      INSERT INTO contradictions (
-        id, entity_id_a, entity_id_b, description, severity,
-        suggested_resolution, status, resolved_action, resolved_at, detected_at
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        this.db.prepare(`
+      INSERT INTO contradictions (
+        id, entity_id_a, entity_id_b, description, severity,
+        suggested_resolution, status, resolved_action, resolved_at, detected_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
     `).run(id, contradiction.entityIds[0], contradiction.entityIds[1], contradiction.description, contradiction.severity, contradiction.suggestedResolution ?? null, contradiction.status, contradiction.resolvedAction ?? null, contradiction.resolvedAt ?? null, contradiction.detectedAt);
         return { ...contradiction, id };
     }
@@ -416,8 +450,8 @@ export class SQLiteStore {
         return rows.map(rowToContradiction);
     }
     async updateContradiction(id, update) {
-        this.db.prepare(`
-      UPDATE contradictions SET status = ?, resolved_action = ?, resolved_at = ? WHERE id = ?
+        this.db.prepare(`
+      UPDATE contradictions SET status = ?, resolved_action = ?, resolved_at = ? WHERE id = ?
     `).run(update.status, update.resolvedAction ?? null, update.resolvedAt ?? null, id);
     }
     // --- Search ---
@@ -426,12 +460,12 @@ export class SQLiteStore {
         const sanitized = text.replace(/[^a-zA-Z0-9\s]/g, ' ').trim();
         if (!sanitized)
             return [];
-        const rows = this.db.prepare(`
-      SELECT e.* FROM entities e
-      JOIN entities_fts fts ON fts.rowid = e.rowid
-      WHERE fts.entities_fts MATCH ? AND e.deleted_at IS NULL
-      ORDER BY rank
-      LIMIT ?
+        const rows = this.db.prepare(`
+      SELECT e.* FROM entities e
+      JOIN entities_fts fts ON fts.rowid = e.rowid
+      WHERE fts.entities_fts MATCH ? AND e.deleted_at IS NULL
+      ORDER BY rank
+      LIMIT ?
     `).all(sanitized, limit);
         return rows.map(rowToEntity);
     }
@@ -476,13 +510,13 @@ export class SQLiteStore {
             }
         }
         // Failed files with error messages
-        const failedFiles = this.db.prepare(`SELECT path, relative_path, parse_error FROM files
-       WHERE status = 'failed' AND parse_error IS NOT NULL
+        const failedFiles = this.db.prepare(`SELECT path, relative_path, parse_error FROM files
+       WHERE status = 'failed' AND parse_error IS NOT NULL
        ORDER BY path LIMIT 50`).all()
             .map((r) => ({ path: r.path, relativePath: r.relative_path, parseError: r.parse_error }));
         // Entity breakdown by type (active only)
-        const entityRows = this.db.prepare(`SELECT type, COUNT(*) as count, AVG(confidence) as avg_confidence
-       FROM entities WHERE deleted_at IS NULL AND status = 'active'
+        const entityRows = this.db.prepare(`SELECT type, COUNT(*) as count, AVG(confidence) as avg_confidence
+       FROM entities WHERE deleted_at IS NULL AND status = 'active'
        GROUP BY type ORDER BY count DESC`).all();
         const entityBreakdown = entityRows.map((r) => ({
             type: r.type, count: r.count, avgConfidence: r.avg_confidence,
@@ -513,14 +547,14 @@ export class SQLiteStore {
                 contradictions.lowSeverity += r.count;
         }
         // Top active contradictions (high first, then medium, limit 10)
-        const topContrRows = this.db.prepare(`SELECT c.id, c.severity, c.description, ea.name as entity_a, eb.name as entity_b
-       FROM contradictions c
-       LEFT JOIN entities ea ON c.entity_id_a = ea.id
-       LEFT JOIN entities eb ON c.entity_id_b = eb.id
-       WHERE c.status = 'active'
-       ORDER BY CASE c.severity
-         WHEN 'critical' THEN 0 WHEN 'high' THEN 1 WHEN 'medium' THEN 2 ELSE 3
-       END, c.detected_at DESC
+        const topContrRows = this.db.prepare(`SELECT c.id, c.severity, c.description, ea.name as entity_a, eb.name as entity_b
+       FROM contradictions c
+       LEFT JOIN entities ea ON c.entity_id_a = ea.id
+       LEFT JOIN entities eb ON c.entity_id_b = eb.id
+       WHERE c.status = 'active'
+       ORDER BY CASE c.severity
+         WHEN 'critical' THEN 0 WHEN 'high' THEN 1 WHEN 'medium' THEN 2 ELSE 3
+       END, c.detected_at DESC
        LIMIT 10`).all();
         const topContradictions = topContrRows.map((r) => ({
             id: r.id.slice(0, 8),
@@ -530,9 +564,9 @@ export class SQLiteStore {
             entityB: r.entity_b ?? 'unknown',
         }));
         // Token estimate from entity extracted_by JSON
-        const tokenRow = this.db.prepare(`SELECT
-        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.input') AS INTEGER)) as total_input,
-        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.output') AS INTEGER)) as total_output
+        const tokenRow = this.db.prepare(`SELECT
+        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.input') AS INTEGER)) as total_input,
+        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.output') AS INTEGER)) as total_output
        FROM entities WHERE deleted_at IS NULL`).get();
         return {
             generatedAt: new Date().toISOString(),
@@ -562,18 +596,18 @@ export class SQLiteStore {
     async integrityCheck() {
         const details = [];
         // Check for orphaned relationships
-        const orphanedRels = this.db.prepare(`
-      SELECT COUNT(*) as count FROM relationships r
-      WHERE NOT EXISTS (SELECT 1 FROM entities WHERE id = r.source_entity_id)
-         OR NOT EXISTS (SELECT 1 FROM entities WHERE id = r.target_entity_id)
+        const orphanedRels = this.db.prepare(`
+      SELECT COUNT(*) as count FROM relationships r
+      WHERE NOT EXISTS (SELECT 1 FROM entities WHERE id = r.source_entity_id)
+         OR NOT EXISTS (SELECT 1 FROM entities WHERE id = r.target_entity_id)
     `).get().count;
         if (orphanedRels > 0) {
             details.push(`Found ${orphanedRels} orphaned relationships`);
         }
         // Check for files referencing missing projects
-        const missingProjects = this.db.prepare(`
-      SELECT COUNT(*) as count FROM files f
-      WHERE NOT EXISTS (SELECT 1 FROM projects WHERE id = f.project_id)
+        const missingProjects = this.db.prepare(`
+      SELECT COUNT(*) as count FROM files f
+      WHERE NOT EXISTS (SELECT 1 FROM projects WHERE id = f.project_id)
     `).get().count;
         if (missingProjects > 0) {
             details.push(`Found ${missingProjects} files referencing missing projects`);
@@ -604,8 +638,8 @@ export class SQLiteStore {
         params.push(limit);
         const entityRows = this.db.prepare(entitySql).all(...params);
         const entityIds = new Set(entityRows.map(e => e.id));
-        const relRows = this.db.prepare(`SELECT id, type, source_entity_id, target_entity_id, confidence
-       FROM relationships
+        const relRows = this.db.prepare(`SELECT id, type, source_entity_id, target_entity_id, confidence
+       FROM relationships
        LIMIT ?`).all(limit * 2);
         // Only include edges where both endpoints are in our node set
         const edges = relRows