@rbalchii/anchor-engine 4.8.0 → 4.8.1

package/engine/dist/services/ingest/watchdog.js

@@ -9,7 +9,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as crypto from 'crypto';
 import { db } from '../../core/db.js';
-import { NOTEBOOK_DIR, PROJECT_ROOT } from '../../config/paths.js';
+import { NOTEBOOK_DIR, PATHS } from '../../config/paths.js';
 import { config } from '../../config/index.js';
 import { pathManager } from '../../utils/path-manager.js';
 import { systemStatus } from '../system-status.js';
@@ -50,8 +50,8 @@ export async function startWatchdog() {
         console.warn(`[Watchdog] Notebook directory not found: ${NOTEBOOK_DIR}. Skipping watch.`);
         return;
     }
-    const inbox = path.join(PROJECT_ROOT, 'inbox');
-    const externalInbox = path.join(PROJECT_ROOT, 'external-inbox');
+    const inbox = PATHS.INBOX_DIR;
+    const externalInbox = PATHS.EXTERNAL_INBOX_DIR;
     // Auto-create inbox directories if missing (Standard 051: Ephemeral Index)
     // These are gitignored and should be created on-demand
     if (!fs.existsSync(inbox)) {
@@ -91,14 +91,7 @@ export async function startWatchdog() {
 export function getWatchedPaths() {
     if (!watcher)
         return [];
-    // chokidar.getWatched() returns an object where keys are paths
-    // But it returns all subdirectories too. We mainly want the roots we added.
-    // For simplicity, we can return the configured roots + static roots.
-    // Better approach: Return the paths explicitly tracked
-    const inbox = path.join(PROJECT_ROOT, 'inbox');
-    const externalInbox = path.join(PROJECT_ROOT, 'external-inbox');
-    const extraPaths = config.WATCHER_EXTRA_PATHS || [];
-    return [inbox, externalInbox, ...extraPaths];
+    return [PATHS.INBOX_DIR, PATHS.EXTERNAL_INBOX_DIR, ...(config.WATCHER_EXTRA_PATHS || [])];
 }
 export async function addWatchPath(newPath) {
     if (!fs.existsSync(newPath)) {
@@ -185,12 +178,9 @@ export async function stopWatchdog() {
  * Get watchdog status
  */
 export function getWatcherStatus() {
-    const inbox = path.join(PROJECT_ROOT, 'inbox');
-    const externalInbox = path.join(PROJECT_ROOT, 'external-inbox');
-    const extraPaths = config.WATCHER_EXTRA_PATHS || [];
     return {
         isRunning: watcher !== null,
-        watchedPaths: [inbox, externalInbox, ...extraPaths]
+        watchedPaths: [PATHS.INBOX_DIR, PATHS.EXTERNAL_INBOX_DIR, ...(config.WATCHER_EXTRA_PATHS || [])]
     };
 }
 /**
@@ -198,8 +188,8 @@ export function getWatcherStatus() {
  */
 export async function triggerManualIngest() {
     try {
-        const inbox = path.join(PROJECT_ROOT, 'inbox');
-        const externalInbox = path.join(PROJECT_ROOT, 'external-inbox');
+        const inbox = PATHS.INBOX_DIR;
+        const externalInbox = PATHS.EXTERNAL_INBOX_DIR;
         if (!fs.existsSync(inbox)) {
             return { status: 'error', message: 'Inbox directory not found' };
         }
@@ -267,9 +257,9 @@ import { AtomicIngestService } from './ingest-atomic.js';
 const atomizer = new AtomizerService();
 const atomicIngest = new AtomicIngestService();
 async function processFile(filePath, event) {
-    // Accept markdown, text, YAML, CSV, JSON, and HTML files
+    // Accept markdown, text, YAML, CSV, JSON, JSONL, and HTML files
     if (!filePath.endsWith('.md') && !filePath.endsWith('.txt') && !filePath.endsWith('.yaml') &&
-        !filePath.endsWith('.csv') && !filePath.endsWith('.json') &&
+        !filePath.endsWith('.csv') && !filePath.endsWith('.json') && !filePath.endsWith('.jsonl') &&
         !filePath.endsWith('.html') && !filePath.endsWith('.htm'))
         return;
     if (filePath.includes('mirrored_brain'))
@@ -352,11 +342,11 @@ async function processFile(filePath, event) {
         // Use the specialized AtomicIngestService for efficiency
         await atomicIngest.ingestResult(compound, molecules, atoms, [bucket]);
         // 6. Update Source Table
-        await db.run(`INSERT INTO sources (path, hash, total_atoms, last_ingest)
-             VALUES ($1, $2, $3, $4)
-             ON CONFLICT (path) DO UPDATE SET
-               hash = EXCLUDED.hash,
-               total_atoms = EXCLUDED.total_atoms,
+        await db.run(`INSERT INTO sources (path, hash, total_atoms, last_ingest)
+             VALUES ($1, $2, $3, $4)
+             ON CONFLICT (path) DO UPDATE SET
+               hash = EXCLUDED.hash,
+               total_atoms = EXCLUDED.total_atoms,
                last_ingest = EXCLUDED.last_ingest`, [
             relativePath,
             fileHash,

package/engine/dist/services/ingest/watchdog.js.map

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package/engine/dist/services/llm/reader.js

@@ -12,16 +12,16 @@ export async function summarizeContext(results, query) {
         return `[Source: ${r.source} ${time}]\n${r.content}`;
     }).join('\n\n---\n\n');
     // 2. Prepare the Reader Prompt
-    const systemPrompt = `You are a Reader for the Sovereign Context Engine.
-Your goal is to read the provided Search Results and create a concise, factual summary that answers the User's Query.
-If the results are irrelevant, state that clearly.
-Focus on extracting dates, decisions, and key patterns.
+    const systemPrompt = `You are a Reader for the Sovereign Context Engine.
+Your goal is to read the provided Search Results and create a concise, factual summary that answers the User's Query.
+If the results are irrelevant, state that clearly.
+Focus on extracting dates, decisions, and key patterns.
 Output ONLY the summary. Do not chat.`;
-    const userPrompt = `USER QUERY: "${query}"
-
-SEARCH RESULTS:
-${docs}
-
+    const userPrompt = `USER QUERY: "${query}"
+
+SEARCH RESULTS:
+${docs}
+
 SUMMARY:`;
     try {
         console.log(`[Reader] Summarizing ${results.length} items for query: "${query}"`);

package/engine/dist/services/mirror/mirror.js

@@ -27,10 +27,10 @@ export async function createMirror() {
         fs.mkdirSync(MIRRORED_BRAIN_PATH, { recursive: true });
     }
     // Join sources with compounds to get cleaned content
-    const sourcesQuery = `
-        SELECT s.path, c.compound_body, c.provenance
-        FROM sources s
-        LEFT JOIN compounds c ON c.path = s.path
+    const sourcesQuery = `
+        SELECT s.path, c.compound_body, c.provenance
+        FROM sources s
+        LEFT JOIN compounds c ON c.path = s.path
     `;
     const result = await db.run(sourcesQuery);
     if (!result.rows || result.rows.length === 0) {
@@ -148,7 +148,7 @@ function getRelativePath(absolutePath) {
     if (!absolutePath)
         return 'unknown_file';
     const inboxDir = PATHS.INBOX_DIR;
-    const externalDir = path.join(path.dirname(PATHS.INBOX_DIR), 'external-inbox');
+    const externalDir = PATHS.EXTERNAL_INBOX_DIR;
     if (absolutePath.startsWith(inboxDir)) {
         return path.relative(inboxDir, absolutePath);
     }

package/engine/dist/services/mirror/mirror.js.map

@@ -1 +1 @@
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+{"version":3,"file":"mirror.js","sourceRoot":"","sources":["../../../src/services/mirror/mirror.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,IAAI,MAAM,SAAS,CAAC;AAC3B,OAAO,EAAE,EAAE,EAAE,MAAM,kBAAkB,CAAC;AACtC,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAC;AACrD,OAAO,KAAK,MAAM,uBAAuB,CAAC;AAE1C,MAAM,CAAC,MAAM,mBAAmB,GAAG,KAAK,CAAC,kBAAkB,CAAC;AAE5D;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,YAAY;IAC9B,OAAO,CAAC,GAAG,CAAC,iEAAiE,CAAC,CAAC;IAE/E,qBAAqB;IACrB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACtC,EAAE,CAAC,SAAS,CAAC,mBAAmB,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3D,CAAC;IAED,qDAAqD;IACrD,MAAM,YAAY,GAAG;;;;KAIpB,CAAC;IACF,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;IAE1C,IAAI,CAAC,MAAM,CAAC,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3C,OAAO,CAAC,GAAG,CAAC,yCAAyC,CAAC,CAAC;QACvD,OAAO;IACX,CAAC;IAED,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,aAAa,GAAG,CAAC,CAAC;IACtB,IAAI,eAAe,GAAG,CAAC,CAAC;IAExB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;QAC5B,MAAM,MAAM,GAAW,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC;QAC9D,MAAM,YAAY,GAAkB,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC;QACpF,MAAM,UAAU,GAAW,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC,IAAI,UAAU,CAAC;QAExF,IAAI,CAAC,MAAM;YAAE,SAAS;QAEtB,gCAAgC;QAChC,IAAI,aAAa,GAAG,QAAQ,CAAC;QAC7B,IAAI,MAAM,CAAC,UAAU,CAAC,gBAAgB,CAAC,IAAI,MAAM,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;YAC3E,aAAa,GAAG,iBAAiB,CAAC;QACtC,CAAC;aAAM,IAAI,MAAM,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;YACzC,aAAa,GAAG,aAAa,CAAC;QAClC,CAAC;QAED,2CAA2C;QAC3C,IAAI,YAAY,EAAE,CAAC;YACf,MAAM,YAAY,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC;YAC7C,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC/E,MAAM,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC;YAC1C,SAAS,EAAE,CAAC;YACZ,SAAS;QACb,CAAC;QAED,wEAAwE;QACxE,IAAI,UAAU,GAAG,MAAM,CAAC;QACxB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;YAC/B,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;QACrD,CAAC;QAED,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC;YAAE,SAAS;QAEzC,4CAA4C;QAC5C,IAAI,UAAU,CAAC,QAAQ,CAAC,OAAO,CAAC,IAAI,UAAU,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;YAC9D,MAAM,UAAU,GAAG,MAAM,gBAAgB,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC;YACrE,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;gBACjB,eAAe,IAAI,UAAU,CAAC;gBAC9B,SAAS;YACb,CAAC;QACL,CAAC;QAED,MAAM,YAAY,GAAG,eAAe,CAAC,UAAU,CAAC,CAAC;QACjD,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;QAC/E,MAAM,QAAQ,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QACvC,aAAa,EAAE,CAAC;IACpB,CAAC;IAED,OAAO,CAAC,GAAG,CAAC,iCAAiC,SAAS,aAAa,aAAa,qBAAqB,eAAe,cAAc,CAAC,CAAC;AACxI,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACnC,YAAoB,EACpB,cAAsB,EACtB,aAAqD,UAAU;IAE/D,OAAO,CAAC,GAAG,CAAC,qCAAqC,YAAY,EAAE,CAAC,CAAC;IACjE,OAAO,CAAC,GAAG,CAAC,iCAAiC,cAAc,EAAE,MAAM,IAAI,CAAC,QAAQ,CAAC,CAAC;IAClF,OAAO,CAAC,GAAG,CAAC,6BAA6B,UAAU,EAAE,CAAC,CAAC;IACvD,OAAO,CAAC,GAAG,CAAC,sCAAsC,mBAAmB,EAAE,CAAC,CAAC;IAEzE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACtC,OAAO,CAAC,GAAG,CAAC,oDAAoD,CAAC,CAAC;QAClE,EAAE,CAAC,SAAS,CAAC,mBAAmB,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACvD,OAAO,CAAC,GAAG,CAAC,mCAAmC,CAAC,CAAC;IACrD,CAAC;IACD,MAAM,UAAU,GAAG,aAAa,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAC3D,OAAO,CAAC,GAAG,CAAC,8BAA8B,UAAU,EAAE,CAAC,CAAC;IAExD,IAAI,CAAC;QACD,MAAM,SAAS,CAAC,UAAU,EAAE,cAAc,CAAC,CAAC;QAC5C,OAAO,CAAC,GAAG,CAAC,oCAAoC,cAAc,EAAE,MAAM,IAAI,CAAC,aAAa,UAAU,EAAE,CAAC,CAAC;IAC1G,CAAC;IAAC,OAAO,KAAU,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CAAC,2BAA2B,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;QAC1D,MAAM,KAAK,CAAC;IAChB,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,KAAK,UAAU,gBAAgB,CAAC,QAAgB,EAAE,aAAqB;IACnE,IAAI,CAAC;QACD,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACnD,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAQ,CAAC;QAEvC,2CAA2C;QAC3C,IAAI,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjE,OAAO,CAAC,CAAC,CAAC,4BAA4B;QAC1C,CAAC;QAED,sDAAsD;QACtD,MAAM,WAAW,GAAG,IAAI,CAAC,iBAAiB;YACtC,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,iBAAiB,CAAC;YACvC,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;QAEtD,OAAO,CAAC,GAAG,CAAC,wBAAwB,QAAQ,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,oBAAoB,WAAW,GAAG,CAAC,CAAC;QAEvG,IAAI,KAAK,GAAG,CAAC,CAAC;QACd,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,OAAO,KAAK,SAAS;gBAAE,SAAS;YAEvD,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CACxB,mBAAmB,EACnB,aAAa,EACb,WAAW,EACX,IAAI,CAAC,IAAI,CACZ,CAAC;YAEF,MAAM,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;YAC1C,KAAK,EAAE,CAAC;QACZ,CAAC;QAED,OAAO,KAAK,CAAC;IACjB,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACT,2DAA2D;QAC3D,OAAO,CAAC,CAAC;IACb,CAAC;AACL,CAAC;AAED;;GAEG;AACH,SAAS,eAAe,CAAC,YAAoB;IACzC,IAAI,CAAC,YAAY;QAAE,OAAO,cAAc,CAAC;IAEzC,MAAM,QAAQ,GAAG,KAAK,CAAC,SAAS,CAAC;IACjC,MAAM,WAAW,GAAG,KAAK,CAAC,kBAAkB,CAAC;IAE7C,IAAI,YAAY,CAAC,UAAU,CAAC,QAAQ,CAAC,E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package/engine/dist/services/research/researcher.js

@@ -55,14 +55,14 @@ export async function fetchAndProcess(url, category = 'article') {
         // Convert
         const markdown = turndownService.turndown(contentHtml);
         // Frontmatter
-        const fileContent = `# ${title}
-> **Source**: ${url}
-> **Date**: ${new Date().toISOString()}
-> **Description**: ${metaDesc}
-
----
-
-${markdown}
+        const fileContent = `# ${title}
+> **Source**: ${url}
+> **Date**: ${new Date().toISOString()}
+> **Description**: ${metaDesc}
+
+---
+
+${markdown}
 `;
         // Filename
         const safeTitle = title.replace(/[^a-zA-Z0-9-_]/g, '_').substring(0, 50);

package/engine/dist/services/scribe/scribe.js

@@ -35,18 +35,18 @@ export async function updateState(history) {
             return { status: 'skipped', message: 'No conversation history to analyze' };
         }
         // 2. Construct the state extraction prompt
-        const prompt = `Analyze this conversation segment and produce a concise "Session State" summary.
-
-Keep it under 200 words. Focus on:
-- Current Goal: What is the user trying to accomplish?
-- Key Decisions: What has been decided or agreed upon?
-- Active Tasks: What work is in progress or pending?
-- Important Context: What background information is critical to remember?
-
-Conversation:
-${recentText}
-
----
+        const prompt = `Analyze this conversation segment and produce a concise "Session State" summary.
+
+Keep it under 200 words. Focus on:
+- Current Goal: What is the user trying to accomplish?
+- Key Decisions: What has been decided or agreed upon?
+- Active Tasks: What work is in progress or pending?
+- Important Context: What background information is critical to remember?
+
+Conversation:
+${recentText}
+
+---
 Session State Summary:`;
         // 3. Generate the state summary
         const inf = getInference();
@@ -56,21 +56,21 @@ Session State Summary:`;
         }
         // 4. Persist to database with special ID
         const timestamp = Date.now();
-        await db.run(`INSERT INTO atoms (id, timestamp, content, source_path, source_id, sequence, type, hash, buckets, epochs, tags, provenance, simhash, embedding)
-             VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14)
-             ON CONFLICT (id) DO UPDATE SET
-               content = EXCLUDED.content,
-               timestamp = EXCLUDED.timestamp,
-               source_path = EXCLUDED.source_path,
-               source_id = EXCLUDED.source_id,
-               sequence = EXCLUDED.sequence,
-               type = EXCLUDED.type,
-               hash = EXCLUDED.hash,
-               buckets = EXCLUDED.buckets,
-               epochs = EXCLUDED.epochs,
-               tags = EXCLUDED.tags,
-               provenance = EXCLUDED.provenance,
-               simhash = EXCLUDED.simhash,
+        await db.run(`INSERT INTO atoms (id, timestamp, content, source_path, source_id, sequence, type, hash, buckets, epochs, tags, provenance, simhash, embedding)
+             VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14)
+             ON CONFLICT (id) DO UPDATE SET
+               content = EXCLUDED.content,
+               timestamp = EXCLUDED.timestamp,
+               source_path = EXCLUDED.source_path,
+               source_id = EXCLUDED.source_id,
+               sequence = EXCLUDED.sequence,
+               type = EXCLUDED.type,
+               hash = EXCLUDED.hash,
+               buckets = EXCLUDED.buckets,
+               epochs = EXCLUDED.epochs,
+               tags = EXCLUDED.tags,
+               provenance = EXCLUDED.provenance,
+               simhash = EXCLUDED.simhash,
                embedding = EXCLUDED.embedding`, [
             SESSION_STATE_ID,
             timestamp,

package/engine/dist/services/search/context-inflator.js

@@ -293,14 +293,14 @@ export class ContextInflator {
         // Atoms are stored with # prefix, but we might search without
         const termWithHash = term.startsWith('#') ? term : `#${term}`;
         const termWithoutHash = term.startsWith('#') ? term.slice(1) : term;
-        let query = `
-            SELECT ap.compound_id, ap.byte_offset, c.path, c.timestamp, c.provenance
-            FROM atom_positions ap
-            JOIN compounds c ON ap.compound_id = c.id
-            WHERE 
-               (LOWER(ap.atom_label) = LOWER($1) 
-               OR LOWER(ap.atom_label) = LOWER($2)
-               OR ap.atom_label ILIKE $3)
+        let query = `
+            SELECT ap.compound_id, ap.byte_offset, c.path, c.timestamp, c.provenance
+            FROM atom_positions ap
+            JOIN compounds c ON ap.compound_id = c.id
+            WHERE 
+               (LOWER(ap.atom_label) = LOWER($1) 
+               OR LOWER(ap.atom_label) = LOWER($2)
+               OR ap.atom_label ILIKE $3)
         `;
         const params = [termWithHash, termWithoutHash, `${termWithoutHash}%`];
         // Apply Provenance Filter
@@ -313,12 +313,12 @@ export class ContextInflator {
             params.push(options.buckets);
             // We join atoms to check if any atom in this compound has the bucket
             // optimize: use EXISTS instead of joining widely
-            query += ` AND EXISTS (
-                SELECT 1 FROM atoms a 
-                WHERE a.compound_id = c.id 
-                AND EXISTS (
-                    SELECT 1 FROM unnest(a.buckets) as b WHERE b = ANY($${params.length})
-                )
+            query += ` AND EXISTS (
+                SELECT 1 FROM atoms a 
+                WHERE a.compound_id = c.id 
+                AND EXISTS (
+                    SELECT 1 FROM unnest(a.buckets) as b WHERE b = ANY($${params.length})
+                )
             )`;
         }
         query += ` ORDER BY c.timestamp DESC LIMIT $${params.length + 1}`;
@@ -357,11 +357,11 @@ export class ContextInflator {
             // So we search for both formats: "#Rob" and "Rob"
             const termWithHash = searchTerm.startsWith('#') ? searchTerm : `#${searchTerm}`;
             const termWithoutHash = searchTerm.startsWith('#') ? searchTerm.slice(1) : searchTerm;
-            let query = `
-                SELECT ap.compound_id, ap.byte_offset, c.path, c.timestamp, c.provenance
-                FROM atom_positions ap
-                JOIN compounds c ON ap.compound_id = c.id
-                WHERE (LOWER(ap.atom_label) = LOWER($1) OR LOWER(ap.atom_label) = LOWER($2))
+            let query = `
+                SELECT ap.compound_id, ap.byte_offset, c.path, c.timestamp, c.provenance
+                FROM atom_positions ap
+                JOIN compounds c ON ap.compound_id = c.id
+                WHERE (LOWER(ap.atom_label) = LOWER($1) OR LOWER(ap.atom_label) = LOWER($2))
             `;
             const params = [termWithHash, termWithoutHash];
             // Apply Provenance Filter
@@ -372,12 +372,12 @@ export class ContextInflator {
             // Apply Bucket Filter
             if (options.buckets && options.buckets.length > 0) {
                 params.push(options.buckets);
-                query += ` AND EXISTS (
-                    SELECT 1 FROM atoms a 
-                    WHERE a.compound_id = c.id 
-                    AND EXISTS (
-                        SELECT 1 FROM unnest(a.buckets) as b WHERE b = ANY($${params.length})
-                    )
+                query += ` AND EXISTS (
+                    SELECT 1 FROM atoms a 
+                    WHERE a.compound_id = c.id 
+                    AND EXISTS (
+                        SELECT 1 FROM unnest(a.buckets) as b WHERE b = ANY($${params.length})
+                    )
                 )`;
             }
             query += ` ORDER BY c.timestamp DESC LIMIT $${params.length + 1}`;
@@ -552,26 +552,26 @@ export class ContextInflator {
         const tagsArray = Array.from(allTags);
         const bucketsArray = Array.from(allBuckets);
         // Query for related content that shares tags or buckets but wasn't in the original results
-        let query = `
-            SELECT id, content, source_path as source, timestamp,
-    buckets, tags, epochs, provenance, simhash as molecular_signature,
-    100 as score  --Lower score for less directly connected content
-            FROM atoms
+        let query = `
+            SELECT id, content, source_path as source, timestamp,
+    buckets, tags, epochs, provenance, simhash as molecular_signature,
+    100 as score  --Lower score for less directly connected content
+            FROM atoms
 WHERE `;
         const params = [];
         const conditions = [];
         // Add conditions for tags if we have any
         if (tagsArray.length > 0) {
-            conditions.push(`EXISTS(
-    SELECT 1 FROM unnest(tags) as tag WHERE tag = ANY($${params.length + 1})
+            conditions.push(`EXISTS(
+    SELECT 1 FROM unnest(tags) as tag WHERE tag = ANY($${params.length + 1})
 )`);
             params.push(tagsArray);
         }
         // Add conditions for buckets if we have any
         if (bucketsArray.length > 0) {
             const bucketParamIndex = params.length + 1;
-            conditions.push(`EXISTS(
-    SELECT 1 FROM unnest(buckets) as bucket WHERE bucket = ANY($${bucketParamIndex})
+            conditions.push(`EXISTS(
+    SELECT 1 FROM unnest(buckets) as bucket WHERE bucket = ANY($${bucketParamIndex})
 )`);
             params.push(bucketsArray);
         }

package/engine/dist/services/search/explore.js

@@ -38,8 +38,8 @@ async function resolveSeedsByQuery(query, limit) {
     if (!terms)
         return [];
     try {
-        const result = await db.run(`SELECT id FROM atoms
-       WHERE to_tsvector('simple', content) @@ to_tsquery('simple', $1)
+        const result = await db.run(`SELECT id FROM atoms
+       WHERE to_tsvector('simple', content) @@ to_tsquery('simple', $1)
        LIMIT $2`, [terms, limit]);
         return result.rows.map(r => r.id);
     }
@@ -64,8 +64,8 @@ async function bfsViaEdges(seeds, maxDepth, minWeight, maxNodes) {
         const nextFrontier = [];
         for (const chunk of chunks) {
             const placeholders = chunk.map((_, i) => `$${i + 2}`).join(', ');
-            const result = await db.run(`SELECT source_id, target_id, weight FROM edges
-         WHERE (source_id IN (${placeholders}) OR target_id IN (${placeholders}))
+            const result = await db.run(`SELECT source_id, target_id, weight FROM edges
+         WHERE (source_id IN (${placeholders}) OR target_id IN (${placeholders}))
            AND weight >= $1`, [minWeight, ...chunk]);
             for (const row of result.rows) {
                 const neighbor = visited.has(row.source_id) ? row.target_id : row.source_id;
@@ -99,9 +99,9 @@ async function bfsViaTags(seeds, maxDepth, maxNodes) {
         const nextFrontier = [];
         for (const chunk of chunks) {
             const placeholders = chunk.map((_, i) => `$${i + 1}`).join(', ');
-            const result = await db.run(`SELECT DISTINCT t2.atom_id
-         FROM tags t1
-         JOIN tags t2 ON t1.tag = t2.tag AND t1.atom_id != t2.atom_id
+            const result = await db.run(`SELECT DISTINCT t2.atom_id
+         FROM tags t1
+         JOIN tags t2 ON t1.tag = t2.tag AND t1.atom_id != t2.atom_id
          WHERE t1.atom_id IN (${placeholders})`, chunk);
             for (const row of result.rows) {
                 if (!visited.has(row.atom_id)) {
@@ -165,14 +165,14 @@ async function edgesTableHasData() {
  * These are the most interconnected nodes in the entire corpus — the spine.
  */
 async function globalTopNodes(seedCount, minWeight) {
-    const result = await db.run(`SELECT id, SUM(weight) AS total_weight
-     FROM (
-       SELECT source_id AS id, weight FROM edges WHERE weight >= $1
-       UNION ALL
-       SELECT target_id AS id, weight FROM edges WHERE weight >= $1
-     ) all_edges
-     GROUP BY id
-     ORDER BY total_weight DESC
+    const result = await db.run(`SELECT id, SUM(weight) AS total_weight
+     FROM (
+       SELECT source_id AS id, weight FROM edges WHERE weight >= $1
+       UNION ALL
+       SELECT target_id AS id, weight FROM edges WHERE weight >= $1
+     ) all_edges
+     GROUP BY id
+     ORDER BY total_weight DESC
      LIMIT $2`, [minWeight, seedCount]);
     return result.rows.map(r => r.id);
 }
@@ -224,11 +224,11 @@ maxCount) {
         const chunk = hubIds.slice(i, i + PGLITE_CHUNK_IDS);
         const placeholders = chunk.map((_, j) => `$${j + 1}`).join(', ');
         const remaining = maxCount - allIds.length;
-        const result = await db.run(`SELECT id FROM atoms
-       WHERE compound_id IN (${placeholders})
-         AND source_path != 'atom_source'
-         AND id NOT LIKE 'mem_%'
-       ORDER BY start_byte
+        const result = await db.run(`SELECT id FROM atoms
+       WHERE compound_id IN (${placeholders})
+         AND source_path != 'atom_source'
+         AND id NOT LIKE 'mem_%'
+       ORDER BY start_byte
        LIMIT ${Math.min(remaining, PGLITE_CHUNK_RESULT_IDS)}`, chunk);
         allIds.push(...result.rows.map((r) => r.id));
     }