feat: port source-first ingestion to os repo

- make source the canonical field across os routes, tools, ui, and mcp
- align fresh-install schema, search, and embedding flows with source-first ingestion

Generated with Claude Code

app/api/extract/pdf/upload/route.ts

@@ -57,10 +57,8 @@ export async function POST(request: NextRequest) {
       headers: { 'Content-Type': 'application/json' },
       body: JSON.stringify({
         title,
-        // Give the description generator and UI a readable summary plus a short excerpt.
-        notes: `Imported PDF document: ${file.name} (${extraction.metadata.pages} pages, ${Math.round(extraction.metadata.text_length / 1000)}k characters).\n\nPreview:\n${extraction.chunk.slice(0, 1200)}`,
-        // Full extracted text goes in chunk for universal chunking/embedding
-        chunk: extraction.chunk,
+        description: `PDF document imported from ${file.name} — ${extraction.metadata.pages} pages of extracted text. Useful as a searchable local source.`,
+        source: extraction.chunk,
         metadata: {
           source: 'pdf_upload',
           original_filename: file.name,

app/api/mcp/route.ts

@@ -134,7 +134,7 @@ function createRAHServer(): McpServer {
               id: node.id,
               title: node.title,
               description: node.description ?? null,
-              notes: node.notes ?? null,
+              source: node.source ?? node.notes ?? null,
               link: node.link ?? null,
               dimensions: node.dimensions || [],
               metadata: node.metadata || {},
@@ -263,21 +263,22 @@ function createRAHServer(): McpServer {
         description: 'Create a new node in the knowledge graph.',
         inputSchema: {
           title: z.string().min(1).max(160).describe('Node title'),
-          content: z.string().max(20000).optional().describe('Node content/notes'),
+          content: z.string().max(20000).optional().describe('Legacy content field; mapped to source'),
+          source: z.string().max(50000).optional().describe('Full source text'),
           link: z.string().url().optional().describe('Source URL'),
           description: z.string().max(2000).optional().describe('Short description'),
           dimensions: z.array(z.string()).min(1).max(5).describe('Categories/tags (at least 1)'),
           metadata: z.record(z.any()).optional().describe('Additional metadata'),
         },
       },
-      async ({ title, content, link, description, dimensions, metadata }) => {
+      async ({ title, content, source, link, description, dimensions, metadata }) => {
         // Call the nodes API internally
         const response = await fetch(`${process.env.NEXT_PUBLIC_BASE_URL || 'http://localhost:3000'}/api/nodes`, {
           method: 'POST',
           headers: { 'Content-Type': 'application/json' },
           body: JSON.stringify({
             title: title.trim(),
-            content: content?.trim(),
+            source: source?.trim() || content?.trim(),
             link: link?.trim(),
             description: description?.trim(),
             dimensions,

app/api/nodes/[id]/regenerate-description/route.ts

@@ -85,7 +85,7 @@ export async function POST(
     // Generate new description using the description service
     const newDescription = await generateDescription({
       title: node.title,
-      notes: node.notes || undefined,
+      notes: node.source || node.description || undefined,
       link: node.link || undefined,
       metadata: enrichedMetadata,
       

app/api/nodes/[id]/route.ts

@@ -85,13 +85,15 @@ export async function PUT(
       updates.dimensions = normalizeDimensions(body.dimensions, 5);
     }
 
-    const incomingChunk = typeof body.chunk === 'string' ? body.chunk : undefined;
-    const incomingNotes = typeof body.notes === 'string' ? body.notes : undefined;
-    const existingChunk = existingNode.chunk ?? '';
+    delete updates.notes;
+    delete updates.chunk;
 
-    if (incomingChunk !== undefined) {
-      const trimmedIncoming = incomingChunk.trim();
-      const trimmedExisting = existingChunk.trim();
+    const incomingSource = typeof body.source === 'string' ? body.source : undefined;
+    const existingSource = existingNode.source ?? '';
+
+    if (incomingSource !== undefined) {
+      const trimmedIncoming = incomingSource.trim();
+      const trimmedExisting = existingSource.trim();
 
       if (!trimmedIncoming) {
         updates.chunk_status = null;
@@ -101,10 +103,6 @@ export async function PUT(
       } else {
         delete updates.chunk_status;
       }
-    } else if (!existingChunk.trim() && hasSufficientContent(incomingNotes)) {
-      updates.chunk = incomingNotes;
-      updates.chunk_status = 'not_chunked';
-      shouldQueueEmbed = true;
     }
 
     const node = await nodeService.updateNode(nodeId, updates);

app/api/nodes/route.ts

@@ -92,15 +92,15 @@ export async function POST(request: NextRequest) {
     // Sanitize title (strip extraction artifacts)
     body.title = sanitizeTitle(body.title);
 
-    const rawNotes = typeof body.notes === 'string' ? body.notes : null;
-    const rawChunk = typeof body.chunk === 'string' ? body.chunk : null;
+    const rawSource = typeof body.source === 'string' ? body.source.trim() : null;
     const eventDate = typeof body.event_date === 'string' ? body.event_date : null;
 
     // Process provided dimensions first (needed for description generation)
     const trimmedProvidedDimensions = normalizeDimensions(body.dimensions, 5);
 
     // Use provided description if present, otherwise auto-generate
-    let nodeDescription: string | undefined = typeof body.description === 'string' && body.description.trim()
+    const isUserSuppliedDescription = typeof body.description === 'string' && body.description.trim().length > 0;
+    let nodeDescription: string | undefined = isUserSuppliedDescription
       ? body.description.trim().slice(0, 280)
       : undefined;
 
@@ -108,7 +108,7 @@ export async function POST(request: NextRequest) {
       try {
         nodeDescription = await generateDescription({
           title: body.title,
-          notes: rawNotes || rawChunk?.slice(0, 2000) || undefined,
+          notes: rawSource?.slice(0, 2000) || undefined,
           link: body.link || undefined,
           metadata: body.metadata,
           dimensions: trimmedProvidedDimensions
@@ -127,7 +127,6 @@ export async function POST(request: NextRequest) {
 
     const descriptionError = validateExplicitDescription(finalDescription);
     if (descriptionError) {
-      const isUserSuppliedDescription = typeof body.description === 'string' && body.description.trim().length > 0;
       if (isUserSuppliedDescription) {
         return NextResponse.json({
           success: false,
@@ -148,33 +147,20 @@ export async function POST(request: NextRequest) {
 
     // Use only provided dimensions (no auto-assignment)
     const finalDimensions = trimmedProvidedDimensions;
-    let chunkToStore = rawChunk;
+    const sourceToStore = rawSource || [body.title, nodeDescription].filter(Boolean).join('\n\n').trim() || null;
     let chunkStatus: Node['chunk_status'];
 
-    if (chunkToStore && chunkToStore.trim().length > 0) {
+    if (sourceToStore && sourceToStore.trim().length > 0) {
       chunkStatus = 'not_chunked';
-    } else {
-      // Build chunk from all available notes if not provided
-      // This ensures every node gets at least one chunk for search
-      const fallbackContent = [body.title, nodeDescription, rawNotes]
-        .filter(Boolean)
-        .join('\n\n')
-        .trim();
-
-      if (fallbackContent) {
-        chunkToStore = fallbackContent;
-        chunkStatus = 'not_chunked';
-      }
     }
 
     const node = await nodeService.createNode({
       title: body.title,
       description: finalDescription,
-      notes: rawNotes ?? undefined,
+      source: sourceToStore ?? undefined,
       event_date: eventDate ?? undefined,
       link: body.link,
       dimensions: finalDimensions,
-      chunk: chunkToStore ?? undefined,
       chunk_status: chunkStatus,
       metadata: body.metadata || {}
     });

apps/mcp-server-standalone/index.js

@@ -77,7 +77,8 @@ All data stays on this device.`;
 // Tool schemas
 const addNodeInputSchema = {
   title: z.string().min(1).max(160).describe('Clear, descriptive title'),
-  content: z.string().max(20000).optional().describe('Node content/notes'),
+  content: z.string().max(20000).optional().describe('Legacy content field; mapped to source'),
+  source: z.string().max(50000).optional().describe('Full source text'),
   link: z.string().url().optional().describe('Source URL'),
   description: z.string().min(24).max(280).describe('REQUIRED. One-sentence summary: WHAT this is (explicit, concrete) + WHY it matters. No weak verbs (discusses, explores, examines). Example: "Podcast — Lex Fridman interviews Sam Altman on AGI timelines. First public comments since board drama."'),
   dimensions: z.array(z.string()).min(1).max(5).describe('1-5 categories. Call queryDimensions first to use existing ones.'),
@@ -354,7 +355,7 @@ async function main() {
       // Note: MCP schema uses "content" for external API compat; mapped to "notes" internally
       inputSchema: addNodeInputSchema
     },
-    async ({ title, content, link, description, dimensions, metadata, chunk }) => {
+    async ({ title, content, source, link, description, dimensions, metadata, chunk }) => {
       const normalizedDimensions = sanitizeDimensions(dimensions);
       if (normalizedDimensions.length === 0) {
         throw new Error('At least one dimension is required.');
@@ -366,12 +367,11 @@ async function main() {
 
       const node = nodeService.createNode({
         title: title.trim(),
-        notes: content?.trim(),
+        source: source?.trim() || chunk?.trim() || content?.trim(),
         link: link?.trim(),
         description: description?.trim(),
         dimensions: normalizedDimensions,
-        metadata: metadata || {},
-        chunk: chunk?.trim()
+        metadata: metadata || {}
       });
 
       const summary = `Created node #${node.id}: ${node.title} [${node.dimensions.join(', ')}]`;
@@ -425,7 +425,7 @@ async function main() {
                 WITH fts_matches AS (
                   SELECT rowid, rank FROM nodes_fts WHERE nodes_fts MATCH ? LIMIT 100
                 )
-                SELECT n.id, n.title, n.description, n.notes, n.link,
+                SELECT n.id, n.title, n.description, n.source, n.link,
                        n.created_at, n.updated_at, n.event_date,
                        COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                                  FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
@@ -446,7 +446,7 @@ async function main() {
                 WITH fts_matches AS (
                   SELECT rowid, rank FROM nodes_fts WHERE nodes_fts MATCH ? LIMIT ?
                 )
-                SELECT n.id, n.title, n.description, n.notes, n.link,
+                SELECT n.id, n.title, n.description, n.source, n.link,
                        n.created_at, n.updated_at, n.event_date,
                        COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                                  FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
@@ -462,7 +462,7 @@ async function main() {
             nodes = rows.map(row => ({
               id: row.id,
               title: row.title,
-              notes: row.notes ?? null,
+              source: row.source ?? null,
               description: row.description ?? null,
               link: row.link ?? null,
               dimensions: JSON.parse(row.dimensions_json || '[]'),
@@ -482,7 +482,7 @@ async function main() {
         const words = trimmedQuery.split(/\s+/).filter(w => w.length > 0);
 
         let sql = `
-          SELECT n.id, n.title, n.description, n.notes, n.link,
+          SELECT n.id, n.title, n.description, n.source, n.link,
                  n.created_at, n.updated_at, n.event_date,
                  COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                            FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
@@ -492,7 +492,7 @@ async function main() {
         const params = [];
 
         for (const word of words) {
-          sql += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+          sql += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
           params.push(`%${word}%`, `%${word}%`, `%${word}%`);
         }
 
@@ -518,7 +518,7 @@ async function main() {
         nodes = rows.map(row => ({
           id: row.id,
           title: row.title,
-          notes: row.notes ?? null,
+          source: row.source ?? null,
           description: row.description ?? null,
           link: row.link ?? null,
           dimensions: JSON.parse(row.dimensions_json || '[]'),
@@ -560,13 +560,13 @@ async function main() {
       for (const id of uniqueIds) {
         const node = nodeService.getNodeById(id);
         if (node) {
-          const rawChunk = node.chunk ?? null;
+          const rawChunk = node.source ?? node.chunk ?? null;
           const chunkTruncated = rawChunk ? rawChunk.length > CHUNK_LIMIT : false;
 
           nodes.push({
             id: node.id,
             title: node.title,
-            notes: node.notes ?? null,
+            source: node.source ?? node.notes ?? null,
             description: node.description ?? null,
             link: node.link ?? null,
             chunk: chunkTruncated ? rawChunk.substring(0, CHUNK_LIMIT) : rawChunk,
@@ -610,14 +610,18 @@ async function main() {
         throw new Error(descriptionError);
       }
 
-      // Map MCP 'content' field → internal 'notes' field
+      // Map MCP legacy fields to canonical source
       const mappedUpdates = { ...updates };
       if (mappedUpdates.content !== undefined) {
-        mappedUpdates.notes = mappedUpdates.content;
-        delete mappedUpdates.content;
+        mappedUpdates.source = mappedUpdates.content;
       }
+      if (mappedUpdates.chunk !== undefined && mappedUpdates.source === undefined) {
+        mappedUpdates.source = mappedUpdates.chunk;
+      }
+      delete mappedUpdates.content;
+      delete mappedUpdates.chunk;
 
-      const node = nodeService.updateNode(id, mappedUpdates, { appendNotes: true });
+      const node = nodeService.updateNode(id, mappedUpdates, { appendNotes: false });
 
       return {
         content: [{ type: 'text', text: `Updated node #${id}` }],

apps/mcp-server-standalone/services/nodeService.js

@@ -9,7 +9,7 @@ function getNodes(filters = {}) {
   const { dimensions, search, limit = 100, offset = 0 } = filters;
 
   let sql = `
-    SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+    SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
            n.created_at, n.updated_at,
            COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                      FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
@@ -30,7 +30,7 @@ function getNodes(filters = {}) {
 
   // Text search
   if (search) {
-    sql += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+    sql += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
     params.push(`%${search}%`, `%${search}%`, `%${search}%`);
   }
 
@@ -70,7 +70,7 @@ function getNodes(filters = {}) {
  */
 function getNodeById(id) {
   const sql = `
-    SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+    SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
            n.created_at, n.updated_at,
            COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                      FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
@@ -108,11 +108,10 @@ function createNode(nodeData) {
   const {
     title: rawTitle,
     description,
-    notes,
+    source,
     link,
     event_date,
     dimensions = [],
-    chunk,
     metadata = {}
   } = nodeData;
 
@@ -121,30 +120,23 @@ function createNode(nodeData) {
   const now = new Date().toISOString();
   const db = getDb();
 
-  // Build chunk fallback from available fields when no explicit chunk provided
-  let chunkToStore = chunk ?? null;
-  if (!chunkToStore || !chunkToStore.trim()) {
-    const fallbackParts = [title, description, notes].filter(Boolean);
-    const fallback = fallbackParts.join('\n\n').trim();
-    if (fallback) {
-      chunkToStore = fallback;
-    }
-  }
+  const sourceToStore = source && source.trim()
+    ? source
+    : [title, description].filter(Boolean).join('\n\n').trim() || null;
 
   const nodeId = transaction(() => {
     const stmt = db.prepare(`
-      INSERT INTO nodes (title, description, notes, link, event_date, metadata, chunk, created_at, updated_at)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+      INSERT INTO nodes (title, description, source, link, event_date, metadata, created_at, updated_at)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?)
     `);
 
     const result = stmt.run(
       title,
       description ?? null,
-      notes ?? null,
+      sourceToStore,
       link ?? null,
       event_date ?? null,
       JSON.stringify(metadata),
-      chunkToStore,
       now,
       now
     );
@@ -169,11 +161,11 @@ function createNode(nodeData) {
 
 /**
  * Update an existing node.
- * Note: notes is APPENDED by default (MCP tool behavior), not replaced.
+ * Source-first update path.
  */
 function updateNode(id, updates, options = {}) {
   const { appendNotes = true } = options;
-  const { title, description, notes, link, event_date, dimensions, chunk, metadata } = updates;
+  const { title, description, source, notes, link, event_date, dimensions, chunk, metadata } = updates;
   const now = new Date().toISOString();
   const db = getDb();
 
@@ -195,15 +187,15 @@ function updateNode(id, updates, options = {}) {
       setFields.push('description = ?');
       params.push(description);
     }
-    if (notes !== undefined) {
-      if (appendNotes && existing.notes) {
-        // Append to existing notes
-        setFields.push('notes = ?');
-        params.push(existing.notes + '\n\n' + notes);
-      } else {
-        setFields.push('notes = ?');
-        params.push(notes);
-      }
+    if (source !== undefined) {
+      setFields.push('source = ?');
+      params.push(source);
+    } else if (notes !== undefined) {
+      const nextSource = appendNotes && existing.source
+        ? `${existing.source}\n\n${notes}`
+        : notes;
+      setFields.push('source = ?');
+      params.push(nextSource);
     }
     if (link !== undefined) {
       setFields.push('link = ?');
@@ -213,8 +205,8 @@ function updateNode(id, updates, options = {}) {
       setFields.push('event_date = ?');
       params.push(event_date);
     }
-    if (chunk !== undefined) {
-      setFields.push('chunk = ?');
+    if (chunk !== undefined && source === undefined) {
+      setFields.push('source = ?');
       params.push(chunk);
     }
     if (metadata !== undefined) {

apps/mcp-server/server.js

@@ -86,6 +86,7 @@ const sanitizeDimensions = (raw) => {
 const addNodeInputSchema = {
   title: z.string().min(1).max(160),
   content: z.string().max(20000).optional(),
+  source: z.string().max(50000).optional(),
   link: z.string().url().optional(),
   description: z.string().max(2000).optional(),
   dimensions: z.array(z.string()).min(1).max(5),
@@ -112,7 +113,7 @@ const searchNodesOutputSchema = {
     z.object({
       id: z.number(),
       title: z.string(),
-      notes: z.string().nullable(),
+      source: z.string().nullable(),
       description: z.string().nullable(),
       link: z.string().nullable(),
       dimensions: z.array(z.string()),
@@ -151,7 +152,7 @@ const getNodesOutputSchema = {
     z.object({
       id: z.number(),
       title: z.string(),
-      notes: z.string().nullable(),
+      source: z.string().nullable(),
       link: z.string().nullable(),
       dimensions: z.array(z.string()),
       updated_at: z.string()
@@ -349,7 +350,7 @@ mcpServer.registerTool(
     inputSchema: addNodeInputSchema,
     outputSchema: addNodeOutputSchema
   },
-  async ({ title, content, link, description, dimensions, metadata, chunk }) => {
+  async ({ title, content, source, link, description, dimensions, metadata, chunk }) => {
     const normalizedDimensions = sanitizeDimensions(dimensions);
     if (normalizedDimensions.length === 0) {
       throw new McpError(
@@ -360,12 +361,11 @@ mcpServer.registerTool(
 
     const payload = {
       title: title.trim(),
-      notes: content?.trim() || undefined,
+      source: source?.trim() || chunk?.trim() || content?.trim() || undefined,
       link: link?.trim() || undefined,
       description: description?.trim() || undefined,
       dimensions: normalizedDimensions,
-      metadata: metadata || {},
-      chunk: chunk?.trim() || undefined
+      metadata: metadata || {}
     };
 
     const result = await callRaHApi('/api/nodes', {
@@ -422,7 +422,7 @@ mcpServer.registerTool(
         nodes: nodes.map((node) => ({
           id: node.id,
           title: node.title,
-          notes: node.notes ?? null,
+          source: node.source ?? node.notes ?? null,
           description: node.description ?? null,
           link: node.link ?? null,
           dimensions: node.dimensions || [],
@@ -446,12 +446,16 @@ mcpServer.registerTool(
       throw new McpError(ErrorCode.InvalidParams, 'At least one field must be provided in updates.');
     }
 
-    // Map MCP 'content' field → internal 'notes' field
+    // Map MCP legacy fields to canonical source
     const mappedUpdates = { ...updates };
     if (mappedUpdates.content !== undefined) {
-      mappedUpdates.notes = mappedUpdates.content;
-      delete mappedUpdates.content;
+      mappedUpdates.source = mappedUpdates.content;
     }
+    if (mappedUpdates.chunk !== undefined && mappedUpdates.source === undefined) {
+      mappedUpdates.source = mappedUpdates.chunk;
+    }
+    delete mappedUpdates.content;
+    delete mappedUpdates.chunk;
 
     const result = await callRaHApi(`/api/nodes/${id}`, {
       method: 'PUT',
@@ -492,7 +496,7 @@ mcpServer.registerTool(
           nodes.push({
             id: result.node.id,
             title: result.node.title,
-            notes: result.node.notes ?? null,
+            source: result.node.source ?? result.node.notes ?? null,
             link: result.node.link ?? null,
             dimensions: result.node.dimensions || [],
             updated_at: result.node.updated_at

apps/mcp-server/stdio-server.js

@@ -35,6 +35,7 @@ const STATUS_PATH = path.join(
 const addNodeInputSchema = {
   title: z.string().min(1).max(160),
   content: z.string().max(20000).optional(),
+  source: z.string().max(50000).optional(),
   link: z.string().url().optional(),
   description: z.string().max(2000).optional(),
   dimensions: z.array(z.string()).min(1).max(5),
@@ -322,7 +323,7 @@ server.registerTool(
     inputSchema: addNodeInputSchema,
     outputSchema: addNodeOutputSchema
   },
-  async ({ title, content, link, description, dimensions, metadata, chunk }) => {
+  async ({ title, content, source, link, description, dimensions, metadata, chunk }) => {
     const normalizedDimensions = sanitizeDimensions(dimensions);
     if (normalizedDimensions.length === 0) {
       throw new Error('At least one dimension/tag is required when creating a node.');
@@ -330,12 +331,11 @@ server.registerTool(
 
     const payload = {
       title: title.trim(),
-      notes: content?.trim() || undefined,
+      source: source?.trim() || chunk?.trim() || content?.trim() || undefined,
       link: link?.trim() || undefined,
       description: description?.trim() || undefined,
       dimensions: normalizedDimensions,
-      metadata: metadata || {},
-      chunk: chunk?.trim() || undefined
+      metadata: metadata || {}
     };
 
     const result = await callRaHApi('/api/nodes', {
@@ -393,7 +393,7 @@ server.registerTool(
         nodes: nodes.map((node) => ({
           id: node.id,
           title: node.title,
-          notes: node.notes ?? null,
+          source: node.source ?? node.notes ?? null,
           description: node.description ?? null,
           link: node.link ?? null,
           dimensions: node.dimensions || [],
@@ -417,12 +417,16 @@ server.registerTool(
       throw new Error('At least one field must be provided in updates.');
     }
 
-    // Map MCP 'content' field → internal 'notes' field
+    // Map MCP legacy fields to canonical source
     const mappedUpdates = { ...updates };
     if (mappedUpdates.content !== undefined) {
-      mappedUpdates.notes = mappedUpdates.content;
-      delete mappedUpdates.content;
+      mappedUpdates.source = mappedUpdates.content;
     }
+    if (mappedUpdates.chunk !== undefined && mappedUpdates.source === undefined) {
+      mappedUpdates.source = mappedUpdates.chunk;
+    }
+    delete mappedUpdates.content;
+    delete mappedUpdates.chunk;
 
     const result = await callRaHApi(`/api/nodes/${id}`, {
       method: 'PUT',
@@ -463,7 +467,7 @@ server.registerTool(
           nodes.push({
             id: result.node.id,
             title: result.node.title,
-            notes: result.node.notes ?? null,
+            source: result.node.source ?? result.node.notes ?? null,
             link: result.node.link ?? null,
             dimensions: result.node.dimensions || [],
             updated_at: result.node.updated_at

docs/2_schema.md

@@ -1,5 +1,7 @@
 # Database Schema
 
+This page describes the database as it exists on disk, including some legacy tables and columns that remain for compatibility and historical records. The current shipped product uses a single RA-H assistant; old delegation-era fields should not be read as active UX concepts.
+
 ## Entity Relationship Diagram
 
 ```mermaid
@@ -8,13 +10,16 @@ erDiagram
     nodes ||--o{ edges : "from"
     nodes ||--o{ edges : "to"
     nodes ||--o{ chunks : "contains"
+    nodes ||--o{ chats : "focused_on"
     dimensions ||--o{ node_dimensions : "tagged_with"
+    chats }o--|| agent_delegations : "belongs_to"
 
     nodes {
         INTEGER id PK
         TEXT title
-        TEXT content
-        TEXT type
+        TEXT source
+        TEXT description
+        TEXT event_date
         BLOB embedding
     }
 
@@ -29,6 +34,7 @@ erDiagram
     dimensions {
         TEXT name PK
         INTEGER is_priority
+        TEXT icon
     }
 
     node_dimensions {
@@ -41,6 +47,19 @@ erDiagram
         INTEGER node_id FK
         TEXT text
     }
+
+    chats {
+        INTEGER id PK
+        INTEGER focused_node_id FK
+        TEXT user_message
+        TEXT assistant_message
+    }
+
+    agent_delegations {
+        INTEGER id PK
+        TEXT task
+        TEXT status
+    }
 ```
 
 ---
@@ -80,25 +99,24 @@ Primary knowledge storage. Each row is a discrete knowledge item.
 **Columns:**
 - `id` (INTEGER PK) - Unique identifier
 - `title` (TEXT) - Node title
-- `content` (TEXT) - Full content
-- `type` (TEXT) - Node type (memory, paper, idea, person, etc)
+- `description` (TEXT) - WHAT this is + WHY it matters (primary identity field)
+- `source` (TEXT) - Canonical source content used for chunking and embedding
 - `link` (TEXT) - External source URL (only for source nodes, not derived ideas)
-- `description` (TEXT) - Brief summary
+- `event_date` (TEXT) - When the thing actually happened (vs `created_at` = when it entered the graph)
 - `metadata` (TEXT) - JSON metadata
-- `chunk` (TEXT) - Source text for chunking
 - `chunk_status` (TEXT) - Chunking status (not_chunked, chunked)
 - `embedding` (BLOB) - Node-level embedding vector
 - `embedding_text` (TEXT) - Text that was embedded
 - `embedding_updated_at` (TEXT) - Embedding timestamp
-- `is_pinned` (INTEGER) - Legacy pin flag (kept for migration; not surfaced in UI)
 - `created_at`, `updated_at` (TEXT) - Timestamps
 
-**Indexes:**
-- `idx_nodes_type` - Fast type filtering
-- `idx_nodes_pinned` - Legacy partial index (no longer recreated, safe to drop later)
+**Temporal dimensions:** Each node has three timestamps:
+- `created_at` - When the node entered the graph (transaction time)
+- `updated_at` - When the node was last modified
+- `event_date` - When the thing actually happened (valid time)
 
 **FTS:**
-- `nodes_fts` - Full-text search on title + content
+- `nodes_fts` - Full-text search on title + source + description
 
 ### edges
 Directed relationships between nodes (knowledge graph).
@@ -117,7 +135,6 @@ Directed relationships between nodes (knowledge graph).
 - `created_at` (TEXT)
 - `context` (TEXT) — JSON blob (canonical; see `EdgeContext` below)
 - `explanation` (TEXT) — legacy column (currently not the canonical source of truth)
-- `user_feedback` (INTEGER) — user rating (not currently used in core flows)
 
 **Indexes:**
 - `idx_edges_from` — fast “outgoing edges” queries
@@ -200,7 +217,8 @@ Master list of categorization tags.
 
 **Columns:**
 - `name` (TEXT PK) - Dimension name
-- `is_priority` (INTEGER) - Priority dimension flag
+- `is_priority` (INTEGER) - Legacy compatibility field retained in schema
+- `icon` (TEXT) - Icon identifier (persisted in database)
 - `updated_at` (TEXT)
 
 ### node_dimensions
@@ -218,12 +236,14 @@ Many-to-many junction table (nodes ↔ dimensions).
 ### chats
 Conversation history with token/cost tracking.
 
+The chat schema still carries some legacy multi-agent fields. Current product framing is simpler: one RA-H assistant, with these columns mainly retained for older records, analytics, and backwards compatibility.
+
 **Columns:**
 - `id` (INTEGER PK)
 - `chat_type` (TEXT) - Conversation type
-- `helper_name` (TEXT) - Agent key (ra-h, ra-h-easy, mini-rah, wise-rah)
-- `agent_type` (TEXT) - Role category (orchestrator, executor, planner)
-- `delegation_id` (INTEGER FK)
+- `helper_name` (TEXT) - Legacy runtime label; current app sessions use `ra-h`
+- `agent_type` (TEXT) - Legacy role field retained for historical rows/analytics
+- `delegation_id` (INTEGER FK) - Legacy link to delegation records
 - `user_message` (TEXT)
 - `assistant_message` (TEXT)
 - `thread_id` (TEXT) - Conversation thread
@@ -235,7 +255,7 @@ Conversation history with token/cost tracking.
 - `idx_chats_thread` - Fast thread retrieval
 
 ### agent_delegations
-Task queue for mini-rah workers.
+Legacy delegation queue from the older multi-agent runtime. Retained so old rows and analytics remain readable; not an active user-facing feature in the current product.
 
 **Columns:**
 - `id` (INTEGER PK)
@@ -248,18 +268,6 @@ Task queue for mini-rah workers.
 - `summary` (TEXT) - Result summary
 - `created_at`, `updated_at` (TEXT)
 
-### chat_memory_state
-Checkpoint tracker for memory pipeline.
-
-**Columns:**
-- `thread_id` (TEXT PK)
-- `helper_name` (TEXT) - Agent that owns the thread
-- `last_processed_chat_id` (INTEGER) - Last chat processed
-- `last_processed_at` (TEXT)
-
-**Indexes:**
-- `idx_chat_memory_thread` - Fast state lookup
-
 ### logs
 Activity audit trail (auto-pruned to last 10k).
 
@@ -316,8 +324,8 @@ Nodes with dimensions aggregated as JSON array.
 
 ```sql
 SELECT 
-  n.id, n.title, n.content, n.link, n.metadata, n.chunk,
-  n.created_at, n.updated_at,
+  n.id, n.title, n.description, n.source, n.link, n.metadata,
+  n.event_date, n.created_at, n.updated_at,
   COALESCE(JSON_GROUP_ARRAY(d.dimension), '[]') AS dimensions_json
 FROM nodes n
 LEFT JOIN node_dimensions d ON d.node_id = n.id

scripts/database/sqlite-ensure-app-schema.sh

@@ -118,13 +118,12 @@ CREATE TABLE nodes (
   id INTEGER PRIMARY KEY,
   title TEXT,
   description TEXT,
-  notes TEXT,
+  source TEXT,
   link TEXT,
   event_date TEXT,
   created_at TEXT,
   updated_at TEXT,
   metadata TEXT,
-  chunk TEXT,
   embedding BLOB,
   embedding_updated_at TEXT,
   embedding_text TEXT,
@@ -281,9 +280,9 @@ if has_table nodes; then
     echo "Adding nodes.metadata"
     "$SQLITE_BIN" "$DB_PATH" "ALTER TABLE nodes ADD COLUMN metadata TEXT;"
   fi
-  if ! has_col nodes chunk; then
-    echo "Adding nodes.chunk"
-    "$SQLITE_BIN" "$DB_PATH" "ALTER TABLE nodes ADD COLUMN chunk TEXT;"
+  if ! has_col nodes source; then
+    echo "Adding nodes.source"
+    "$SQLITE_BIN" "$DB_PATH" "ALTER TABLE nodes ADD COLUMN source TEXT;"
   fi
   # is_pinned removed in final schema pass
 fi

src/components/focus/FocusPanel.tsx

@@ -9,10 +9,10 @@ import { parseNodeMarkers } from '@/tools/infrastructure/nodeFormatter';
 import { Node, NodeConnection, Chunk } from '@/types/database';
 import DimensionTags from './dimensions/DimensionTags';
 import { getNodeIcon } from '@/utils/nodeIcons';
-import { openExternalUrl, shouldOpenExternally } from '@/utils/openExternalUrl';
 import { useDimensionIcons } from '@/context/DimensionIconsContext';
 import ConfirmDialog from '../common/ConfirmDialog';
 import { SourceReader } from './source';
+import { openExternalUrl, shouldOpenExternally } from '@/utils/openExternalUrl';
 
 
 interface NodeSearchResult {
@@ -36,8 +36,8 @@ interface FocusPanelProps {
 }
 
 export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeClick, onTabClose, refreshTrigger, onOpenInOtherSlot, hideTabBar, onTextSelect, highlightedPassage }: FocusPanelProps) {
-  const { dimensionIcons } = useDimensionIcons();
   const [nodesData, setNodesData] = useState<Record<number, Node>>({});
+  const { dimensionIcons } = useDimensionIcons();
 
   // Context menu state
   const [contextMenu, setContextMenu] = useState<{ x: number; y: number; tabId: number } | null>(null); 
@@ -97,10 +97,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   const [chunkExpanded, setChunkExpanded] = useState<{ [key: number]: boolean }>({});
   
   // Edges expand/collapse state
-  // edgesExpanded removed — all connections shown in Edges tab
-  
-  // Connections section collapsed state (default closed)
-  const [edgeSearchOpen, setEdgeSearchOpen] = useState(false);
+  const [edgesExpanded, setEdgesExpanded] = useState<{ [key: number]: boolean }>({});
   
   // Title expanded state for click-to-expand full title
   const [titleExpanded, setTitleExpanded] = useState<{ [key: number]: boolean }>({});
@@ -108,7 +105,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   // Description regeneration state
   const [regeneratingDescription, setRegeneratingDescription] = useState<number | null>(null);
 
-  // Content tab state: 'notes', 'desc', or 'source'
+  // Content tab state: 'desc', 'notes', 'edges', or 'source'
   const [activeContentTab, setActiveContentTab] = useState<'notes' | 'desc' | 'edges' | 'source'>('desc');
 
   // Desc (description) edit mode state
@@ -135,6 +132,9 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   const [loadingChunks, setLoadingChunks] = useState<Set<number>>(new Set());
   const [chunksExpanded, setChunksExpanded] = useState<Record<number, boolean>>({});
 
+  // Edge creation search toggle
+  const [edgeSearchOpen, setEdgeSearchOpen] = useState(false);
+
   // Helper: preview edge type based on heuristics (mirrors backend logic)
   const previewEdgeType = (explanation: string): { type: string; label: string } | null => {
     const norm = (explanation || '').trim().toLowerCase();
@@ -230,13 +230,16 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
     setEditingField(null);
     setEditingValue('');
     setEditingNodeId(null);
-    // Also clear notes/desc/source edit modes
+    // Also clear notes/desc/source/edges edit modes
     setNotesEditMode(false);
     setNotesEditValue('');
     setDescEditMode(false);
     setDescEditValue('');
     setSourceEditMode(false);
     setSourceEditValue('');
+    setEdgeSearchOpen(false);
+    setNodeSearchQuery('');
+    setNodeSearchSuggestions([]);
   }, [activeTab]);
 
   const fetchNodeData = async (id: number) => {
@@ -356,7 +359,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       const updateData: Record<string, string> = {};
 
       if (editingField === 'notes') {
-        updateData.content = editingValue;
+        updateData.notes = editingValue;
       } else {
         updateData[editingField] = editingValue;
       }
@@ -378,7 +381,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
         setNodesData(prev => ({ ...prev, [nodeId]: result.node }));
       }
 
-      // Safety net: ensure edges exist for any tokens present in saved content
+      // Safety net: ensure edges exist for any tokens present in saved notes
       if (editingField === 'notes' && typeof editingValue === 'string') {
         try {
           const tokens = parseNodeMarkers(editingValue);
@@ -421,7 +424,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       const response = await fetch(`/api/nodes/${nodeId}`, {
         method: 'PUT',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ notes: contentValue }),
+        body: JSON.stringify({ content: contentValue }),
       });
       if (!response.ok) throw new Error('Failed to save');
       const result = await response.json();
@@ -497,16 +500,16 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
     setDescEditMode(true);
   };
 
-  // Sync description to source (chunk) and re-embed
+  // Sync description to source and re-embed
   const syncDescToSource = async () => {
     if (!activeTab) return;
     setDescSaving(true);
     try {
-      // Save description to chunk field
+      // Save description to source field
       const response = await fetch(`/api/nodes/${activeTab}`, {
         method: 'PUT',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ chunk: descEditValue }),
+        body: JSON.stringify({ source: descEditValue }),
       });
       if (!response.ok) throw new Error('Failed to sync');
       const result = await response.json();
@@ -533,7 +536,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
     }
   };
 
-  // Save notes (content) with explicit Save button
+  // Save notes-tab content into canonical source
   const saveNotes = async () => {
     if (!activeTab) return;
     setNotesSaving(true);
@@ -541,7 +544,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       const response = await fetch(`/api/nodes/${activeTab}`, {
         method: 'PUT',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ notes: notesEditValue }),
+        body: JSON.stringify({ source: notesEditValue }),
       });
       if (!response.ok) throw new Error('Failed to save');
       const result = await response.json();
@@ -571,8 +574,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       setNotesEditMode(false);
       setNotesEditValue('');
     } catch (e) {
-      console.error('Error saving notes:', e);
-      alert('Failed to save notes. Please try again.');
+      console.error('Error saving source content:', e);
+      alert('Failed to save content. Please try again.');
     } finally {
       setNotesSaving(false);
     }
@@ -587,11 +590,11 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   // Start editing notes
   const startNotesEdit = () => {
     if (!activeTab || !nodesData[activeTab]) return;
-    setNotesEditValue(nodesData[activeTab].notes || '');
+    setNotesEditValue(nodesData[activeTab].source || nodesData[activeTab].notes || '');
     setNotesEditMode(true);
   };
 
-  // Save source (chunk) with explicit Save button
+  // Save source with explicit Save button
   const saveSource = async () => {
     if (!activeTab) return;
     setSourceSaving(true);
@@ -599,7 +602,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       const response = await fetch(`/api/nodes/${activeTab}`, {
         method: 'PUT',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ chunk: sourceEditValue }),
+        body: JSON.stringify({ source: sourceEditValue }),
       });
       if (!response.ok) throw new Error('Failed to save');
       const result = await response.json();
@@ -625,7 +628,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   // Start editing source
   const startSourceEdit = () => {
     if (!activeTab || !nodesData[activeTab]) return;
-    setSourceEditValue(nodesData[activeTab].chunk || '');
+    setSourceEditValue(nodesData[activeTab].source || nodesData[activeTab].chunk || '');
     setSourceEditMode(true);
   };
 
@@ -641,11 +644,11 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
     setSyncing(true);
     setShowSyncConfirm(false);
     try {
-      // First, save notes content to chunk field
+      // First, save notes content to source field
       const response = await fetch(`/api/nodes/${activeTab}`, {
         method: 'PUT',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ chunk: notesEditValue }),
+        body: JSON.stringify({ source: notesEditValue }),
       });
       if (!response.ok) throw new Error('Failed to sync');
       const result = await response.json();
@@ -997,14 +1000,14 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
   const embedContent = async (nodeId: number) => {
     const node = nodesData[nodeId];
     const hasNotes = node?.notes?.trim();
-    const hasChunk = node?.chunk?.trim();
-    // If chunk is empty but content exists, auto-populate chunk from content
-    if (!hasChunk && hasNotes) {
+    const hasSource = (node?.source || node?.chunk)?.trim();
+    // If source is empty but notes exist, auto-populate source from notes
+    if (!hasSource && hasNotes) {
       try {
         const response = await fetch(`/api/nodes/${nodeId}`, {
           method: 'PUT',
           headers: { 'Content-Type': 'application/json' },
-          body: JSON.stringify({ chunk: hasNotes })
+          body: JSON.stringify({ source: hasNotes })
         });
         
         if (response.ok) {
@@ -1014,13 +1017,13 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
           }
         }
       } catch (error) {
-        console.error('Failed to auto-populate chunk for embedding:', error);
+        console.error('Failed to auto-populate source for embedding:', error);
         return;
       }
     }
-    // If neither content nor chunk exist, require content
-    if (!hasNotes && !hasChunk) {
-      startEdit('content', '');
+    // If neither notes nor source exist, require notes
+    if (!hasNotes && !hasSource) {
+      startEdit('notes', '');
       return;
     }
     setEmbeddingNode(nodeId);
@@ -1119,7 +1122,6 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       setAddingEdge(null);
       setEdgeExplanation('');
       setPendingEdgeTarget(null);
-      setEdgeSearchOpen(false);
 
     } catch (error) {
       console.error('Error creating edge:', error);
@@ -1157,7 +1159,6 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
       setPendingEdgeTarget(null);
       setNodeSearchQuery('');
       setNodeSearchSuggestions([]);
-      setEdgeSearchOpen(false);
 
     } catch (error) {
       console.error('Error creating edge:', error);
@@ -1277,63 +1278,55 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 borderRadius: '8px',
                 maxHeight: '200px',
                 overflowY: 'auto',
-                zIndex: 10,
-                boxShadow: '0 8px 24px rgba(0, 0, 0, 0.4)'
+                zIndex: 100,
+                boxShadow: '0 8px 24px rgba(0, 0, 0, 0.5)',
               }}>
                 {nodeSearchSuggestions.map((suggestion, index) => (
                   <div
                     key={suggestion.id}
-                    onClick={() => handleSelectNodeSuggestion(suggestion)}
+                    onClick={() => {
+                      handleSelectNodeSuggestion(suggestion);
+                      setNodeSearchQuery('');
+                      setNodeSearchSuggestions([]);
+                      setEdgeSearchOpen(false);
+                    }}
                     style={{
-                      padding: '10px 14px',
+                      padding: '8px 12px',
                       cursor: 'pointer',
-                      borderBottom: index < nodeSearchSuggestions.length - 1 ? '1px solid var(--rah-bg-active)' : 'none',
+                      borderBottom: index < nodeSearchSuggestions.length - 1 ? '1px solid var(--rah-border)' : 'none',
                       background: index === selectedSearchIndex ? 'var(--rah-bg-active)' : 'transparent',
                       transition: 'background 100ms ease',
                       display: 'flex',
                       alignItems: 'center',
-                      gap: '10px'
-                    }}
-                    onMouseEnter={(e) => {
-                      if (index !== selectedSearchIndex) {
-                        e.currentTarget.style.background = 'var(--rah-bg-active)';
-                      }
-                    }}
-                    onMouseLeave={(e) => {
-                      if (index !== selectedSearchIndex) {
-                        e.currentTarget.style.background = 'transparent';
-                      }
+                      gap: '8px',
                     }}
+                    onMouseEnter={(e) => { e.currentTarget.style.background = 'var(--rah-bg-active)'; }}
+                    onMouseLeave={(e) => { if (index !== selectedSearchIndex) e.currentTarget.style.background = 'transparent'; }}
                   >
                     <span style={{
-                      display: 'inline-flex',
-                      alignItems: 'center',
-                      justifyContent: 'center',
                       fontSize: '9px',
                       fontWeight: 600,
-                      color: 'var(--rah-bg-base)',
-                      background: '#22c55e',
-                      padding: '3px 6px',
-                      borderRadius: '6px',
-                      minWidth: '24px',
-                      textAlign: 'center',
+                      color: 'var(--rah-text-inverse)',
+                      background: 'var(--rah-accent-green)',
+                      padding: '2px 5px',
+                      borderRadius: '4px',
                       flexShrink: 0,
-                      fontFamily: "'SF Mono', 'Fira Code', monospace"
+                      fontFamily: "'SF Mono', 'Fira Code', monospace",
                     }}>
                       {suggestion.id}
                     </span>
                     <span style={{
-                      fontSize: '13px',
+                      fontSize: '12px',
                       color: 'var(--rah-text-base)',
                       overflow: 'hidden',
                       textOverflow: 'ellipsis',
                       whiteSpace: 'nowrap',
-                      flex: 1
+                      flex: 1,
                     }}>
                       {suggestion.title}
                     </span>
                     {index === selectedSearchIndex && (
-                      <span style={{ color: 'var(--rah-text-muted)', fontSize: '13px' }}>↵</span>
+                      <span style={{ color: 'var(--rah-text-muted)', fontSize: '12px' }}>↵</span>
                     )}
                   </div>
                 ))}
@@ -1342,10 +1335,10 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
           </div>
         )}
 
-        {/* Connections List */}
+        {/* Connections list */}
         <div style={{ flex: 1, overflowY: 'auto' }}>
           {loadingEdges.has(activeTab) ? (
-            <div style={{ color: 'var(--rah-text-muted)', fontSize: '12px', fontStyle: 'italic', padding: '16px 0', textAlign: 'center' }}>Loading connections…</div>
+            <div style={{ color: 'var(--rah-text-muted)', fontSize: '12px', fontStyle: 'italic', padding: '8px 0' }}>Loading connections…</div>
           ) : (() => {
             const list = edgesData[activeTab] || [];
             if (list.length === 0) {
@@ -1358,18 +1351,18 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     key={connection.id}
                     style={{
                       padding: '6px 0',
-                      borderBottom: '1px solid var(--rah-bg-panel)',
+                      borderBottom: '1px solid var(--rah-border)',
                       display: 'flex',
                       flexDirection: 'column',
                       gap: '2px',
                       minWidth: 0,
                     }}
                   >
-                    {/* Row 1: arrow + ID + icon + title + delete */}
+                    {/* Row 1: arrow + ID + title + delete */}
                     <div style={{ display: 'flex', alignItems: 'center', gap: '6px', minWidth: 0 }}>
                       <span style={{
                         fontSize: '11px',
-                        color: connection.edge.from_node_id === activeTab ? '#22c55e' : '#f59e0b',
+                        color: connection.edge.from_node_id === activeTab ? 'var(--rah-accent-green)' : '#f59e0b',
                         fontWeight: 600,
                         width: '14px',
                         textAlign: 'center',
@@ -1380,8 +1373,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                       <span style={{
                         fontSize: '9px',
                         fontWeight: 700,
-                        color: 'var(--rah-bg-base)',
-                        background: '#22c55e',
+                        color: 'var(--rah-text-inverse)',
+                        background: 'var(--rah-accent-green)',
                         padding: '1px 5px',
                         borderRadius: '4px',
                         flexShrink: 0,
@@ -1405,7 +1398,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                           minWidth: 0,
                           cursor: 'pointer',
                         }}
-                        onMouseEnter={(e) => { e.currentTarget.style.color = '#22c55e'; }}
+                        onMouseEnter={(e) => { e.currentTarget.style.color = 'var(--rah-accent-green)'; }}
                         onMouseLeave={(e) => { e.currentTarget.style.color = 'var(--rah-text-base)'; }}
                       >
                         {connection.connected_node.title}
@@ -1414,7 +1407,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         onClick={() => deleteEdge(connection.edge.id)}
                         disabled={deletingEdge === connection.edge.id}
                         style={{
-                          color: 'var(--rah-border-stronger)',
+                          color: 'var(--rah-text-muted)',
                           fontSize: '14px',
                           background: 'transparent',
                           border: 'none',
@@ -1424,7 +1417,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                           lineHeight: 1,
                         }}
                         onMouseEnter={(e) => { if (deletingEdge !== connection.edge.id) e.currentTarget.style.color = '#dc2626'; }}
-                        onMouseLeave={(e) => { if (deletingEdge !== connection.edge.id) e.currentTarget.style.color = 'var(--rah-border-stronger)'; }}
+                        onMouseLeave={(e) => { if (deletingEdge !== connection.edge.id) e.currentTarget.style.color = 'var(--rah-text-muted)'; }}
                       >
                         {deletingEdge === connection.edge.id ? '...' : '×'}
                       </button>
@@ -1464,8 +1457,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                           disabled={edgeSavingId === connection.edge.id}
                           style={{
                             fontSize: '10px',
-                            color: '#000',
-                            background: '#22c55e',
+                            color: 'var(--rah-text-inverse)',
+                            background: 'var(--rah-accent-green)',
                             border: 'none',
                             borderRadius: '4px',
                             padding: '3px 8px',
@@ -1508,9 +1501,9 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         {typeof connection.edge.context?.type === 'string' && (
                           <span style={{
                             fontSize: '9px',
-                            color: 'var(--rah-text-muted)',
+                            color: 'var(--rah-text-soft)',
                             background: 'var(--rah-bg-active)',
-                            border: '1px solid var(--rah-bg-active)',
+                            border: '1px solid var(--rah-border)',
                             padding: '1px 5px',
                             borderRadius: '999px',
                             flexShrink: 0,
@@ -1522,7 +1515,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         <span
                           style={{
                             fontSize: '11px',
-                            color: connection.edge.context?.explanation ? '#777' : '#444',
+                            color: connection.edge.context?.explanation ? 'var(--rah-text-muted)' : 'var(--rah-text-soft)',
                             fontStyle: connection.edge.context?.explanation ? 'normal' : 'italic',
                             overflow: 'hidden',
                             textOverflow: 'ellipsis',
@@ -1594,7 +1587,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
         <div style={{
           display: 'flex',
           borderBottom: '1px solid var(--rah-border)',
-          background: 'var(--rah-bg-surface)',
+          background: 'var(--rah-bg-base)',
           flexShrink: 0,
           overflowX: 'auto',
           overflowY: 'hidden'
@@ -1631,7 +1624,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     display: 'flex',
                     alignItems: 'center',
                     borderRight: '1px solid var(--rah-border)',
-                    background: isActive ? 'var(--rah-bg-subtle)' : 'var(--rah-bg-surface)',
+                    background: isActive ? 'var(--rah-bg-subtle)' : 'var(--rah-bg-base)',
                     borderBottom: isActive ? '2px solid var(--rah-text-muted)' : 'none',
                     paddingBottom: isActive ? '0' : '2px',
                     minWidth: '120px',
@@ -1646,7 +1639,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                       padding: '8px 12px',
                       fontSize: '12px',
                       fontFamily: 'inherit',
-                      color: isActive ? 'var(--rah-text-active)' : 'var(--rah-text-muted)',
+                      color: isActive ? 'var(--rah-text-active)' : 'var(--rah-text-soft)',
                       background: 'transparent',
                       border: 'none',
                       cursor: 'pointer',
@@ -1708,7 +1701,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
             Loading...
           </div>
         ) : !currentNode ? (
-          <div style={{ color: 'var(var(--rah-text-muted))', fontSize: '13px' }}>Node not found.</div>
+          <div style={{ color: 'var(--rah-text-muted)', fontSize: '13px' }}>Node not found.</div>
         ) : nodesData[activeTab] ? (
           <div style={{ height: '100%', display: 'flex', flexDirection: 'column' }}>
             {/* URL Row - Above Title */}
@@ -1791,8 +1784,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         return;
                       }
 
-                      const link = nodesData[activeTab].link;
-                      if (!link || !shouldOpenExternally(link)) {
+                      const link = nodesData[activeTab].link || '';
+                      if (!shouldOpenExternally(link)) {
                         return;
                       }
 
@@ -1819,7 +1812,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                   <span
                     onClick={() => startEdit('link', '')}
                     style={{
-                      color: 'var(--rah-text-muted)',
+                      color: '#555',
                       fontSize: '11px',
                       cursor: 'pointer',
                       fontStyle: 'italic'
@@ -1850,8 +1843,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 }}
                 style={{
                   display: 'inline-block',
-                  background: '#22c55e',
-                  color: 'var(--rah-bg-base)',
+                  background: 'var(--rah-accent-green)',
+                  color: 'var(--rah-text-inverse)',
                   fontSize: '10px',
                   fontWeight: 600,
                   padding: '2px 6px',
@@ -1864,7 +1857,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 {activeTab}
               </span>
 
-              {/* Node type icon */}
+              {/* Node icon */}
               {nodesData[activeTab] && (
                 <span style={{ flexShrink: 0, display: 'flex', alignItems: 'center' }}>
                   {getNodeIcon(nodesData[activeTab], dimensionIcons, 18)}
@@ -1938,7 +1931,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                   title={titleExpanded[activeTab] ? undefined : (nodesData[activeTab].title || 'Untitled')}
                 >
                   {nodesData[activeTab].title || 'Untitled'}
-                  {savingField === 'title' && <span style={{ color: 'var(--rah-text-muted)', fontSize: '10px', marginLeft: '6px' }}>saving...</span>}
+                  {savingField === 'title' && <span style={{ color: '#555', fontSize: '10px', marginLeft: '6px' }}>saving...</span>}
                 </h1>
               )}
 
@@ -1948,14 +1941,14 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 style={{
                   display: 'flex',
                   alignItems: 'center',
-                  gap: '4px',
+                  gap: '6px',
                   padding: '4px 8px',
                   fontSize: '10px',
                   fontWeight: 500,
-                  color: activeContentTab === 'edges' ? '#22c55e' : 'var(--rah-text-muted)',
+                  color: activeContentTab === 'edges' ? 'var(--rah-accent-green)' : 'var(--rah-text-muted)',
                   background: activeContentTab === 'edges' ? '#0f2417' : 'transparent',
                   border: '1px solid',
-                  borderColor: activeContentTab === 'edges' ? '#22c55e' : 'var(--rah-border-strong)',
+                  borderColor: activeContentTab === 'edges' ? 'var(--rah-accent-green)' : 'var(--rah-border-strong)',
                   borderRadius: '4px',
                   cursor: 'pointer',
                   transition: 'all 0.2s',
@@ -1963,7 +1956,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 }}
                 onMouseEnter={(e) => {
                   if (activeContentTab !== 'edges') {
-                    e.currentTarget.style.color = '#22c55e';
+                    e.currentTarget.style.color = 'var(--rah-accent-green)';
                     e.currentTarget.style.borderColor = '#166534';
                   }
                 }}
@@ -1983,18 +1976,18 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                       style={{
                         minWidth: '18px',
                         height: '18px',
+                        padding: '0 6px',
                         borderRadius: '999px',
                         display: 'inline-flex',
                         alignItems: 'center',
                         justifyContent: 'center',
-                        padding: '0 6px',
-                        background: activeContentTab === 'edges' ? 'rgba(34, 197, 94, 0.18)' : 'var(--rah-bg-active)',
-                        color: activeContentTab === 'edges' ? '#a7f3b8' : 'var(--rah-text-muted)',
+                        background: activeContentTab === 'edges' ? 'var(--rah-accent-green-soft)' : 'var(--rah-bg-active)',
+                        color: activeContentTab === 'edges' ? 'var(--rah-accent-green)' : 'var(--rah-text-soft)',
                         fontSize: '10px',
                         lineHeight: 1,
                       }}
                     >
-                      {(edgesData[activeTab] || []).length}
+                      {edgesData[activeTab]?.length ?? 0}
                     </span>
                   </span>
                 )}
@@ -2084,7 +2077,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                 borderBottom: '1px solid var(--rah-border)'
               }}>
                 <button
-                  onClick={() => { setActiveContentTab('desc'); setNotesEditMode(false); setSourceEditMode(false); }}
+                  onClick={() => { setActiveContentTab('desc'); setNotesEditMode(false); setSourceEditMode(false); setEdgeSearchOpen(false); }}
                   style={{
                     padding: '8px 16px',
                     fontSize: '11px',
@@ -2092,7 +2085,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     color: activeContentTab === 'desc' ? 'var(--rah-text-base)' : 'var(--rah-text-muted)',
                     background: 'transparent',
                     border: 'none',
-                    borderBottom: activeContentTab === 'desc' ? '2px solid #22c55e' : '2px solid transparent',
+                    borderBottom: activeContentTab === 'desc' ? '2px solid var(--rah-accent-green)' : '2px solid transparent',
                     cursor: 'pointer',
                     transition: 'all 0.15s',
                     marginBottom: '-1px'
@@ -2101,7 +2094,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                   Desc
                 </button>
                 <button
-                  onClick={() => { setActiveContentTab('notes'); setDescEditMode(false); setSourceEditMode(false); }}
+                  onClick={() => { setActiveContentTab('notes'); setDescEditMode(false); setSourceEditMode(false); setEdgeSearchOpen(false); }}
                   style={{
                     padding: '8px 16px',
                     fontSize: '11px',
@@ -2109,7 +2102,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     color: activeContentTab === 'notes' ? 'var(--rah-text-base)' : 'var(--rah-text-muted)',
                     background: 'transparent',
                     border: 'none',
-                    borderBottom: activeContentTab === 'notes' ? '2px solid #22c55e' : '2px solid transparent',
+                    borderBottom: activeContentTab === 'notes' ? '2px solid var(--rah-accent-green)' : '2px solid transparent',
                     cursor: 'pointer',
                     transition: 'all 0.15s',
                     marginBottom: '-1px'
@@ -2126,13 +2119,13 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     color: activeContentTab === 'edges' ? 'var(--rah-text-base)' : 'var(--rah-text-muted)',
                     background: 'transparent',
                     border: 'none',
-                    borderBottom: activeContentTab === 'edges' ? '2px solid #22c55e' : '2px solid transparent',
+                    borderBottom: activeContentTab === 'edges' ? '2px solid var(--rah-accent-green)' : '2px solid transparent',
                     cursor: 'pointer',
                     transition: 'all 0.15s',
                     marginBottom: '-1px'
                   }}
                 >
-                  Edges{activeTab && edgesData[activeTab]?.length ? ` (${edgesData[activeTab].length})` : ''}
+                  Edges
                 </button>
                 <button
                   onClick={() => { setActiveContentTab('source'); setDescEditMode(false); setNotesEditMode(false); setEdgeSearchOpen(false); }}
@@ -2143,7 +2136,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     color: activeContentTab === 'source' ? 'var(--rah-text-base)' : 'var(--rah-text-muted)',
                     background: 'transparent',
                     border: 'none',
-                    borderBottom: activeContentTab === 'source' ? '2px solid #22c55e' : '2px solid transparent',
+                    borderBottom: activeContentTab === 'source' ? '2px solid var(--rah-accent-green)' : '2px solid transparent',
                     cursor: 'pointer',
                     transition: 'all 0.15s',
                     marginBottom: '-1px'
@@ -2164,7 +2157,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         gap: '4px',
                         padding: '4px 8px',
                         fontSize: '10px',
-                        color: 'var(--rah-text-muted)',
+                        color: 'var(--rah-text-soft)',
                         background: 'transparent',
                         border: '1px solid var(--rah-border-strong)',
                         borderRadius: '4px',
@@ -2183,7 +2176,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         gap: '4px',
                         padding: '4px 8px',
                         fontSize: '10px',
-                        color: 'var(--rah-text-muted)',
+                        color: 'var(--rah-text-soft)',
                         background: 'transparent',
                         border: '1px solid var(--rah-border-strong)',
                         borderRadius: '4px',
@@ -2208,7 +2201,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         gap: '4px',
                         padding: '4px 8px',
                         fontSize: '10px',
-                        color: '#22c55e',
+                        color: 'var(--rah-accent-green)',
                         background: 'transparent',
                         border: '1px solid #166534',
                         borderRadius: '4px',
@@ -2227,7 +2220,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         gap: '4px',
                         padding: '4px 8px',
                         fontSize: '10px',
-                        color: 'var(--rah-text-muted)',
+                        color: 'var(--rah-text-soft)',
                         background: 'transparent',
                         border: '1px solid var(--rah-border-strong)',
                         borderRadius: '4px',
@@ -2268,8 +2261,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                         gap: '4px',
                         padding: '4px 8px',
                         fontSize: '10px',
-                        color: edgeSearchOpen ? '#000' : '#22c55e',
-                        background: edgeSearchOpen ? '#22c55e' : 'transparent',
+                        color: edgeSearchOpen ? 'var(--rah-text-inverse)' : 'var(--rah-accent-green)',
+                        background: edgeSearchOpen ? 'var(--rah-accent-green)' : 'transparent',
                         border: '1px solid #166534',
                         borderRadius: '4px',
                         cursor: 'pointer',
@@ -2383,7 +2376,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               gap: '4px',
                               padding: '6px 12px',
                               fontSize: '11px',
-                              color: 'var(--rah-text-muted)',
+                              color: 'var(--rah-text-soft)',
                               background: 'transparent',
                               border: '1px solid var(--rah-border-strong)',
                               borderRadius: '4px',
@@ -2402,8 +2395,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               gap: '4px',
                               padding: '6px 12px',
                               fontSize: '11px',
-                              color: '#000',
-                              background: '#22c55e',
+                              color: 'var(--rah-text-inverse)',
+                              background: 'var(--rah-accent-green)',
                               border: 'none',
                               borderRadius: '4px',
                               cursor: 'pointer',
@@ -2433,7 +2426,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     <div
                       onClick={startDescEdit}
                       style={{
-                        color: 'var(--rah-text-muted)',
+                        color: '#555',
                         fontSize: '12px',
                         fontStyle: 'italic',
                         cursor: 'pointer',
@@ -2536,7 +2529,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                             top: '50px',
                             left: '12px',
                             background: 'var(--rah-bg-active)',
-                            border: '1px solid var(--rah-border-stronger)',
+                            border: '1px solid var(--rah-border-strong)',
                             borderRadius: '6px',
                             zIndex: 1000,
                             maxHeight: '200px',
@@ -2566,11 +2559,11 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                                     fontSize: '13px',
                                     color: 'var(--rah-text-base)',
                                     cursor: 'pointer',
-                                    background: idx === mentionIndex ? 'var(--rah-bg-hover)' : 'transparent',
+                                    background: idx === mentionIndex ? 'var(--rah-bg-elevated)' : 'transparent',
                                     borderBottom: idx < mentionResults.length - 1 ? '1px solid var(--rah-border-strong)' : 'none'
                                   }}
                                 >
-                                  <span style={{ color: '#22c55e', marginRight: '8px', fontWeight: 600 }}>{n.id}</span>
+                                  <span style={{ color: 'var(--rah-accent-green)', marginRight: '8px', fontWeight: 600 }}>{n.id}</span>
                                   <span>{n.title.length > 50 ? n.title.slice(0, 50) + '…' : n.title}</span>
                                 </div>
                               ))
@@ -2621,7 +2614,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               gap: '4px',
                               padding: '6px 12px',
                               fontSize: '11px',
-                              color: 'var(--rah-text-muted)',
+                              color: 'var(--rah-text-soft)',
                               background: 'transparent',
                               border: '1px solid var(--rah-border-strong)',
                               borderRadius: '4px',
@@ -2640,8 +2633,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               gap: '4px',
                               padding: '6px 12px',
                               fontSize: '11px',
-                              color: '#000',
-                              background: '#22c55e',
+                              color: 'var(--rah-text-inverse)',
+                              background: 'var(--rah-accent-green)',
                               border: 'none',
                               borderRadius: '4px',
                               cursor: 'pointer',
@@ -2671,7 +2664,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               style={{
                                 padding: '4px 10px',
                                 fontSize: '11px',
-                                color: 'var(--rah-text-muted)',
+                                color: 'var(--rah-text-soft)',
                                 background: 'transparent',
                                 border: '1px solid var(--rah-border-strong)',
                                 borderRadius: '4px',
@@ -2685,7 +2678,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               style={{
                                 padding: '4px 10px',
                                 fontSize: '11px',
-                                color: '#000',
+                                color: 'var(--rah-text-inverse)',
                                 background: '#f59e0b',
                                 border: 'none',
                                 borderRadius: '4px',
@@ -2711,7 +2704,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                       }}
                     >
                       <MarkdownWithNodeTokens
-                        content={nodesData[activeTab].notes || ''}
+                        content={nodesData[activeTab].notes}
                         onNodeClick={onNodeClick || onTabSelect}
                       />
                     </div>
@@ -2719,7 +2712,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                     <div
                       onClick={startNotesEdit}
                       style={{
-                        color: 'var(--rah-text-muted)',
+                        color: '#555',
                         fontSize: '12px',
                         fontStyle: 'italic',
                         cursor: 'pointer',
@@ -2814,7 +2807,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                             gap: '4px',
                             padding: '6px 12px',
                             fontSize: '11px',
-                            color: 'var(--rah-text-muted)',
+                            color: 'var(--rah-text-soft)',
                             background: 'transparent',
                             border: '1px solid var(--rah-border-strong)',
                             borderRadius: '4px',
@@ -2833,8 +2826,8 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                             gap: '4px',
                             padding: '6px 12px',
                             fontSize: '11px',
-                            color: '#000',
-                            background: '#22c55e',
+                            color: 'var(--rah-text-inverse)',
+                            background: 'var(--rah-accent-green)',
                             border: 'none',
                             borderRadius: '4px',
                             cursor: 'pointer',
@@ -2861,7 +2854,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                           display: 'flex',
                           background: 'var(--rah-bg-surface)',
                           borderRadius: '4px',
-                          border: '1px solid var(--rah-bg-active)',
+                          border: '1px solid var(--rah-border)',
                           overflow: 'hidden',
                         }}>
                           <button
@@ -2871,7 +2864,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               fontSize: '10px',
                               fontWeight: 500,
                               color: sourceReaderMode === 'raw' ? 'var(--rah-text-active)' : 'var(--rah-text-muted)',
-                              background: sourceReaderMode === 'raw' ? 'var(--rah-border-strong)' : 'transparent',
+                              background: sourceReaderMode === 'raw' ? 'var(--rah-bg-active)' : 'transparent',
                               border: 'none',
                               cursor: 'pointer',
                               transition: 'all 0.15s ease',
@@ -2886,7 +2879,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                               fontSize: '10px',
                               fontWeight: 500,
                               color: sourceReaderMode === 'reader' ? 'var(--rah-text-active)' : 'var(--rah-text-muted)',
-                              background: sourceReaderMode === 'reader' ? 'var(--rah-border-strong)' : 'transparent',
+                              background: sourceReaderMode === 'reader' ? 'var(--rah-bg-active)' : 'transparent',
                               border: 'none',
                               cursor: 'pointer',
                               transition: 'all 0.15s ease',
@@ -2907,17 +2900,17 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                             fontSize: '10px',
                             color: 'var(--rah-text-muted)',
                             background: 'transparent',
-                            border: '1px solid var(--rah-bg-active)',
+                            border: '1px solid var(--rah-border)',
                             borderRadius: '4px',
                             cursor: 'pointer',
                           }}
                           onMouseEnter={(e) => {
-                            e.currentTarget.style.color = 'var(--rah-text-secondary)';
-                            e.currentTarget.style.borderColor = 'var(--rah-border-stronger)';
+                            e.currentTarget.style.color = 'var(--rah-text-soft)';
+                            e.currentTarget.style.borderColor = 'var(--rah-border-strong)';
                           }}
                           onMouseLeave={(e) => {
                             e.currentTarget.style.color = 'var(--rah-text-muted)';
-                            e.currentTarget.style.borderColor = 'var(--rah-bg-active)';
+                            e.currentTarget.style.borderColor = 'var(--rah-border)';
                           }}
                         >
                           <Pencil size={10} />
@@ -2927,10 +2920,10 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
 
                       {/* Content display */}
                       <div style={{ flex: 1, overflow: 'auto' }}>
-                        {nodesData[activeTab]?.chunk ? (
+                        {(nodesData[activeTab]?.source || nodesData[activeTab]?.chunk) ? (
                           sourceReaderMode === 'reader' ? (
                             <SourceReader 
-                              content={nodesData[activeTab].chunk} 
+                              content={nodesData[activeTab].source || nodesData[activeTab].chunk || ''} 
                               onTextSelect={onTextSelect ? (text) => onTextSelect(activeTab, nodesData[activeTab]?.title || 'Untitled', text) : undefined}
                               highlightedText={highlightedPassage?.nodeId === activeTab ? highlightedPassage.selectedText : null}
                             />
@@ -2949,7 +2942,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
                                 minHeight: '100%',
                               }}
                             >
-                              {nodesData[activeTab].chunk}
+                              {nodesData[activeTab].source || nodesData[activeTab].chunk}
                             </div>
                           )
                         ) : (
@@ -3036,7 +3029,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
               textAlign: 'left',
             }}
             onMouseEnter={(e) => {
-              e.currentTarget.style.background = 'var(--rah-border-strong)';
+              e.currentTarget.style.background = 'var(--rah-bg-elevated)';
               e.currentTarget.style.color = 'var(--rah-text-active)';
             }}
             onMouseLeave={(e) => {
@@ -3068,7 +3061,7 @@ export default function FocusPanel({ openTabs, activeTab, onTabSelect, onNodeCli
             textAlign: 'left',
           }}
           onMouseEnter={(e) => {
-            e.currentTarget.style.background = 'var(--rah-border-strong)';
+            e.currentTarget.style.background = 'var(--rah-bg-elevated)';
             e.currentTarget.style.color = 'var(--rah-text-active)';
           }}
           onMouseLeave={(e) => {

src/components/layout/ThreePanelLayout.tsx

@@ -172,12 +172,12 @@ export default function ThreePanelLayout() {
         id: node.id,
         title: node.title,
         link: node.link,
+        source: node.source,
         notes: node.notes,
         dimensions: node.dimensions,
         created_at: node.created_at,
         updated_at: node.updated_at,
         chunk_status: node.chunk_status,
-        chunk: node.chunk,
         metadata: node.metadata,
       }));
       setOpenTabsData(validNodes);

src/components/views/DatabaseTableView.tsx

@@ -175,13 +175,13 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
           <div style={{
             display: 'flex',
             alignItems: 'center',
-            background: 'var(var(--rah-bg-surface))',
-            border: '1px solid var(--rah-border-strong)',
+            background: 'var(--rah-bg-base)',
+            border: '1px solid var(--rah-border)',
             borderRadius: '6px',
             padding: '0 8px',
             gap: '6px',
           }}>
-            <Search size={12} style={{ color: 'var(var(--rah-text-muted))', flexShrink: 0 }} />
+            <Search size={12} style={{ color: 'var(--rah-text-muted)', flexShrink: 0 }} />
             <input
               type="text"
               value={searchQuery}
@@ -190,7 +190,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
               style={{
                 background: 'transparent',
                 border: 'none',
-                color: 'var(var(--rah-text-active))',
+                color: 'var(--rah-text-active)',
                 fontSize: '12px',
                 padding: '5px 0',
                 outline: 'none',
@@ -201,7 +201,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
               <button
                 type="button"
                 onClick={() => { setSearchQuery(''); setActiveSearch(''); }}
-                style={{ background: 'transparent', border: 'none', color: 'var(var(--rah-text-muted))', cursor: 'pointer', padding: 0, display: 'flex' }}
+                style={{ background: 'transparent', border: 'none', color: 'var(--rah-text-muted)', cursor: 'pointer', padding: 0, display: 'flex' }}
               >
                 <X size={11} />
               </button>
@@ -236,8 +236,8 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
               style={{
                 display: 'flex', alignItems: 'center', gap: '4px',
                 padding: '4px 7px', background: 'transparent',
-                border: '1px solid var(--rah-border-strong)', borderRadius: '5px',
-                color: 'var(var(--rah-text-muted))', fontSize: '11px', cursor: 'pointer',
+                border: '1px solid var(--rah-border)', borderRadius: '5px',
+                color: 'var(--rah-text-soft)', fontSize: '11px', cursor: 'pointer',
               }}
               onMouseEnter={(e) => { e.currentTarget.style.background = 'rgba(255,255,255,0.04)'; }}
               onMouseLeave={(e) => { e.currentTarget.style.background = 'transparent'; }}
@@ -249,7 +249,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
             {showFilterPicker && (
               <div style={{
                 position: 'absolute', top: '100%', left: 0, marginTop: '4px',
-                background: 'var(var(--rah-bg-panel))', border: '1px solid var(--rah-border-strong)', borderRadius: '10px',
+                background: 'var(--rah-bg-panel)', border: '1px solid var(--rah-border)', borderRadius: '10px',
                 padding: '6px', minWidth: '220px', maxHeight: '320px', overflowY: 'auto',
                 zIndex: 1000, boxShadow: '0 8px 24px rgba(0,0,0,0.4)',
               }}>
@@ -260,13 +260,13 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                   placeholder="Search dimensions..."
                   autoFocus
                   style={{
-                    width: '100%', padding: '7px 10px', background: 'var(var(--rah-bg-surface))',
+                    width: '100%', padding: '7px 10px', background: 'var(--rah-bg-base)',
                     border: '1px solid transparent', borderRadius: '6px',
-                    color: 'var(var(--rah-text-active))', fontSize: '12px', marginBottom: '4px', outline: 'none',
+                    color: 'var(--rah-text-active)', fontSize: '12px', marginBottom: '4px', outline: 'none',
                   }}
                 />
                 {filterPickerDimensions.length === 0 ? (
-                  <div style={{ padding: '12px', color: 'var(var(--rah-text-muted))', fontSize: '12px', textAlign: 'center' }}>
+                  <div style={{ padding: '12px', color: 'var(--rah-text-muted)', fontSize: '12px', textAlign: 'center' }}>
                     No matching dimensions
                   </div>
                 ) : (
@@ -283,14 +283,14 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                       style={{
                         display: 'flex', alignItems: 'center', justifyContent: 'space-between',
                         width: '100%', padding: '7px 10px', background: 'transparent',
-                        border: 'none', borderRadius: '5px', color: 'var(var(--rah-text-secondary))',
+                        border: 'none', borderRadius: '5px', color: 'var(--rah-text-secondary)',
                         fontSize: '12px', cursor: 'pointer', textAlign: 'left',
                       }}
                       onMouseEnter={(e) => { e.currentTarget.style.background = 'rgba(255,255,255,0.04)'; }}
                       onMouseLeave={(e) => { e.currentTarget.style.background = 'transparent'; }}
                     >
                       <span>{d.dimension}</span>
-                      <span style={{ color: 'var(var(--rah-text-muted))', fontSize: '10px', background: 'var(var(--rah-bg-active))', padding: '1px 6px', borderRadius: '10px' }}>
+                      <span style={{ color: 'var(--rah-text-muted)', fontSize: '10px', background: 'var(--rah-bg-active)', padding: '1px 6px', borderRadius: '10px' }}>
                         {d.count}
                       </span>
                     </button>
@@ -303,9 +303,9 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
           {selectedFilters.length > 0 && (
             <button
               onClick={() => setSelectedFilters([])}
-              style={{ padding: '4px 6px', background: 'transparent', border: 'none', color: 'var(var(--rah-text-muted))', fontSize: '11px', cursor: 'pointer' }}
+              style={{ padding: '4px 6px', background: 'transparent', border: 'none', color: 'var(--rah-text-muted)', fontSize: '11px', cursor: 'pointer' }}
               onMouseEnter={(e) => { e.currentTarget.style.color = '#ef4444'; }}
-              onMouseLeave={(e) => { e.currentTarget.style.color = '#666'; }}
+              onMouseLeave={(e) => { e.currentTarget.style.color = 'var(--rah-text-muted)'; }}
             >
               Clear
             </button>
@@ -319,8 +319,8 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
             style={{
               display: 'flex', alignItems: 'center', gap: '4px',
               padding: '4px 7px', background: 'transparent',
-              border: '1px solid var(--rah-border-strong)', borderRadius: '5px',
-              color: 'var(var(--rah-text-muted))', fontSize: '11px', cursor: 'pointer', whiteSpace: 'nowrap',
+              border: '1px solid var(--rah-border)', borderRadius: '5px',
+              color: 'var(--rah-text-soft)', fontSize: '11px', cursor: 'pointer', whiteSpace: 'nowrap',
             }}
             onMouseEnter={(e) => { e.currentTarget.style.background = 'rgba(255,255,255,0.04)'; }}
             onMouseLeave={(e) => { e.currentTarget.style.background = 'transparent'; }}
@@ -333,7 +333,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
           {showSortDropdown && (
             <div style={{
               position: 'absolute', top: '100%', right: 0, marginTop: '4px',
-              background: 'var(var(--rah-bg-panel))', border: '1px solid var(--rah-border-strong)', borderRadius: '10px',
+              background: 'var(--rah-bg-panel)', border: '1px solid var(--rah-border)', borderRadius: '10px',
               padding: '4px', minWidth: '160px', zIndex: 1000,
               boxShadow: '0 8px 24px rgba(0,0,0,0.4)',
             }}>
@@ -346,13 +346,13 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     width: '100%', padding: '7px 10px',
                     background: sortOrder === key ? 'rgba(255,255,255,0.04)' : 'transparent',
                     border: 'none', borderRadius: '5px',
-                    color: sortOrder === key ? '#f0f0f0' : '#999',
+                    color: sortOrder === key ? 'var(--rah-text-active)' : 'var(--rah-text-soft)',
                     fontSize: '12px', cursor: 'pointer', textAlign: 'left',
                   }}
                   onMouseEnter={(e) => { e.currentTarget.style.background = 'rgba(255,255,255,0.04)'; }}
                   onMouseLeave={(e) => { e.currentTarget.style.background = sortOrder === key ? 'rgba(255,255,255,0.04)' : 'transparent'; }}
                 >
-                  {sortOrder === key && <span style={{ color: '#22c55e', fontSize: '12px' }}>✓</span>}
+                  {sortOrder === key && <span style={{ color: 'var(--rah-accent-green)', fontSize: '12px' }}>✓</span>}
                   {SORT_LABELS[key]}
                 </button>
               ))}
@@ -363,15 +363,15 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
         {/* Pagination */}
         <div style={{
           display: 'flex', alignItems: 'center', gap: '6px',
-          fontSize: '11px', color: 'var(var(--rah-text-muted))', whiteSpace: 'nowrap',
+          fontSize: '11px', color: 'var(--rah-text-muted)', whiteSpace: 'nowrap',
         }}>
           <span>{total > 0 ? `${startItem}-${endItem} of ${total}` : '0 nodes'}</span>
           <button
             onClick={() => setPage(p => Math.max(1, p - 1))}
             disabled={page <= 1}
             style={{
-              background: 'transparent', border: '1px solid var(--rah-border-strong)', borderRadius: '4px',
-              color: page <= 1 ? '#333' : '#888', cursor: page <= 1 ? 'default' : 'pointer',
+              background: 'transparent', border: '1px solid var(--rah-border)', borderRadius: '4px',
+              color: page <= 1 ? 'var(--rah-text-muted)' : 'var(--rah-text-soft)', cursor: page <= 1 ? 'default' : 'pointer',
               padding: '2px 4px', display: 'flex',
             }}
           >
@@ -381,8 +381,8 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
             onClick={() => setPage(p => Math.min(totalPages, p + 1))}
             disabled={page >= totalPages}
             style={{
-              background: 'transparent', border: '1px solid var(--rah-border-strong)', borderRadius: '4px',
-              color: page >= totalPages ? '#333' : '#888',
+              background: 'transparent', border: '1px solid var(--rah-border)', borderRadius: '4px',
+              color: page >= totalPages ? 'var(--rah-text-muted)' : 'var(--rah-text-soft)',
               cursor: page >= totalPages ? 'default' : 'pointer',
               padding: '2px 4px', display: 'flex',
             }}
@@ -410,9 +410,9 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
       {/* Table */}
       <div style={{ flex: 1, overflow: 'auto' }}>
         {loading ? (
-          <div style={{ padding: '40px', color: 'var(var(--rah-text-muted))', textAlign: 'center', fontSize: '13px' }}>Loading...</div>
+          <div style={{ padding: '40px', color: 'var(--rah-text-muted)', textAlign: 'center', fontSize: '13px' }}>Loading...</div>
         ) : nodes.length === 0 ? (
-          <div style={{ padding: '40px', color: 'var(var(--rah-text-muted))', textAlign: 'center', fontSize: '13px' }}>
+          <div style={{ padding: '40px', color: 'var(--rah-text-muted)', textAlign: 'center', fontSize: '13px' }}>
             {activeSearch || selectedFilters.length > 0 ? 'No nodes match your filters.' : 'No nodes yet.'}
           </div>
         ) : (
@@ -450,15 +450,15 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                       height: '44px',
                       cursor: 'pointer',
                       background: hoveredRow === node.id
-                        ? '#141414'
-                        : i % 2 === 0 ? '#080808' : '#0d0d0d',
+                        ? 'var(--rah-bg-panel)'
+                        : i % 2 === 0 ? 'var(--rah-bg-base)' : 'var(--rah-bg-subtle)',
                       transition: 'background 0.1s ease',
                     }}
                   >
                     {/* Title */}
                     <td style={tdStyle()}>
                       <div style={truncCell}>
-                        <span style={{ fontSize: '13px', color: '#e0e0e0', fontWeight: 400 }}>
+                        <span style={{ fontSize: '13px', color: 'var(--rah-text-base)', fontWeight: 400 }}>
                           {node.title || 'Untitled'}
                         </span>
                       </div>
@@ -468,7 +468,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     <td style={tdStyle({ textAlign: 'right' })}>
                       <span style={{
                         fontFamily: 'ui-monospace, SFMono-Regular, "SF Mono", Menlo, monospace',
-                        fontSize: '11px', color: 'var(var(--rah-text-muted))',
+                        fontSize: '11px', color: 'var(--rah-text-muted)',
                       }}>
                         {node.id}
                       </span>
@@ -477,7 +477,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     {/* Description */}
                     <td style={tdStyle()}>
                       <div style={truncCell}>
-                        <span style={{ fontSize: '11px', color: 'var(var(--rah-text-muted))' }}>
+                        <span style={{ fontSize: '11px', color: 'var(--rah-text-soft)' }}>
                           {node.description || '\u2014'}
                         </span>
                       </div>
@@ -486,8 +486,8 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     {/* Notes */}
                     <td style={tdStyle()}>
                       <div style={truncCell}>
-                        <span style={{ fontSize: '11px', color: 'var(var(--rah-text-muted))' }}>
-                          {node.notes ? node.notes.slice(0, 120) : '\u2014'}
+                        <span style={{ fontSize: '11px', color: 'var(--rah-text-soft)' }}>
+                          {(node.source || node.notes) ? (node.source || node.notes || '').slice(0, 120) : '\u2014'}
                         </span>
                       </div>
                     </td>
@@ -503,7 +503,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                             </span>
                           </span>
                         ) : (
-                          <span style={{ fontSize: '11px', color: '#333' }}>{'\u2014'}</span>
+                          <span style={{ fontSize: '11px', color: 'var(--rah-text-muted)' }}>{'\u2014'}</span>
                         )}
                       </div>
                     </td>
@@ -516,49 +516,49 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                             {node.dimensions.slice(0, 3).map(d => (
                               <span key={d} style={{
                                 fontSize: '9px', padding: '1px 5px',
-                                background: '#111914', border: '1px solid #1f2f24',
-                                color: '#bbf7d0', borderRadius: '3px',
+                                background: 'var(--rah-accent-green-soft)', border: '1px solid var(--rah-accent-green-soft-strong)',
+                                color: 'var(--rah-accent-green)', borderRadius: '3px',
                                 whiteSpace: 'nowrap',
                               }}>
                                 {d}
                               </span>
                             ))}
                             {node.dimensions.length > 3 && (
-                              <span style={{ fontSize: '9px', color: 'var(var(--rah-text-muted))' }}>
+                              <span style={{ fontSize: '9px', color: 'var(--rah-text-muted)' }}>
                                 +{node.dimensions.length - 3}
                               </span>
                             )}
                           </>
                         ) : (
-                          <span style={{ fontSize: '10px', color: '#333' }}>{'\u2014'}</span>
+                          <span style={{ fontSize: '10px', color: 'var(--rah-text-muted)' }}>{'\u2014'}</span>
                         )}
                       </div>
                     </td>
 
                     {/* Edges */}
                     <td style={tdStyle({ textAlign: 'right' })}>
-                      <span style={{ fontSize: '12px', color: node.edge_count ? '#888' : '#333' }}>
+                      <span style={{ fontSize: '12px', color: node.edge_count ? 'var(--rah-text-soft)' : 'var(--rah-text-muted)' }}>
                         {node.edge_count ?? 0}
                       </span>
                     </td>
 
                     {/* Event Date */}
                     <td style={tdStyle()}>
-                      <span style={{ fontSize: '11px', color: node.event_date ? '#888' : '#333' }}>
+                      <span style={{ fontSize: '11px', color: node.event_date ? 'var(--rah-text-soft)' : 'var(--rah-text-muted)' }}>
                         {formatDate(node.event_date)}
                       </span>
                     </td>
 
                     {/* Updated */}
                     <td style={tdStyle()}>
-                      <span style={{ fontSize: '11px', color: 'var(var(--rah-text-muted))' }}>
+                      <span style={{ fontSize: '11px', color: 'var(--rah-text-muted)' }}>
                         {formatRelativeTime(node.updated_at)}
                       </span>
                     </td>
 
                     {/* Created */}
                     <td style={tdStyle()}>
-                      <span style={{ fontSize: '11px', color: 'var(var(--rah-text-muted))' }}>
+                      <span style={{ fontSize: '11px', color: 'var(--rah-text-muted)' }}>
                         {formatRelativeTime(node.created_at)}
                       </span>
                     </td>
@@ -566,7 +566,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     {/* Metadata */}
                     <td style={tdStyle()}>
                       <div style={truncCell}>
-                        <span style={{ fontSize: '10px', color: 'var(var(--rah-text-muted))', fontFamily: 'ui-monospace, SFMono-Regular, "SF Mono", Menlo, monospace' }}>
+                        <span style={{ fontSize: '10px', color: 'var(--rah-text-muted)', fontFamily: 'ui-monospace, SFMono-Regular, "SF Mono", Menlo, monospace' }}>
                           {metaStr || '\u2014'}
                         </span>
                       </div>
@@ -575,8 +575,8 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     {/* Chunk */}
                     <td style={tdStyle()}>
                       <div style={truncCell}>
-                        <span style={{ fontSize: '10px', color: 'var(var(--rah-text-muted))' }}>
-                          {node.chunk ? node.chunk.slice(0, 100) : '\u2014'}
+                        <span style={{ fontSize: '10px', color: 'var(--rah-text-muted)' }}>
+                          {(node.source || node.chunk) ? (node.source || node.chunk || '').slice(0, 100) : '\u2014'}
                         </span>
                       </div>
                     </td>
@@ -585,7 +585,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
                     <td style={tdStyle()}>
                       <span style={{
                         fontSize: '10px',
-                        color: node.chunk_status === 'chunked' ? '#4a9' : node.chunk_status === 'error' ? '#e55' : '#555',
+                        color: node.chunk_status === 'chunked' ? 'var(--rah-accent-green)' : node.chunk_status === 'error' ? '#e55' : 'var(--rah-text-muted)',
                       }}>
                         {node.chunk_status || '\u2014'}
                       </span>
@@ -593,7 +593,7 @@ export default function DatabaseTableView({ onNodeClick, refreshToken = 0, toolb
 
                     {/* Embedding Updated */}
                     <td style={tdStyle()}>
-                      <span style={{ fontSize: '11px', color: 'var(var(--rah-text-muted))' }}>
+                      <span style={{ fontSize: '11px', color: 'var(--rah-text-muted)' }}>
                         {node.embedding_updated_at ? formatRelativeTime(node.embedding_updated_at) : '\u2014'}
                       </span>
                     </td>
@@ -612,15 +612,15 @@ function thStyle(extra: React.CSSProperties = {}): React.CSSProperties {
   return {
     position: 'sticky' as const,
     top: 0,
-    background: 'var(var(--rah-bg-base))',
+    background: 'var(--rah-bg-base)',
     padding: '8px 12px',
     fontSize: '10px',
     fontWeight: 500,
-    color: 'var(var(--rah-text-muted))',
+    color: 'var(--rah-text-muted)',
     textAlign: 'left',
     letterSpacing: '0.05em',
     whiteSpace: 'nowrap',
-    borderBottom: '1px solid rgba(255,255,255,0.06)',
+    borderBottom: '1px solid var(--rah-border)',
     zIndex: 1,
     ...extra,
   };
@@ -630,7 +630,7 @@ function tdStyle(extra: React.CSSProperties = {}): React.CSSProperties {
   return {
     padding: '0 12px',
     verticalAlign: 'middle',
-    borderBottom: '1px solid #111',
+    borderBottom: '1px solid var(--rah-border)',
     overflow: 'hidden',
     ...extra,
   };

src/components/views/GridView.tsx

@@ -104,7 +104,7 @@ export default function GridView({ nodes, onNodeClick }: GridViewProps) {
               </div>
 
               {/* Description or Content Preview */}
-              {(node.description || node.notes) && (
+              {(node.description || node.source || node.notes) && (
                 <div style={{
                   flex: 1,
                   fontSize: '11px',
@@ -116,7 +116,7 @@ export default function GridView({ nodes, onNodeClick }: GridViewProps) {
                   WebkitBoxOrient: 'vertical',
                   marginBottom: '10px'
                 }}>
-                  {node.description || truncateContent(node.notes)}
+                  {node.description || truncateContent(node.source || node.notes)}
                 </div>
               )}
 

src/components/views/ListView.tsx

@@ -105,7 +105,7 @@ export default function ListView({ nodes, onNodeClick }: ListViewProps) {
               </div>
 
               {/* Description or Content Preview */}
-              {(node.description || node.notes) && (
+              {(node.description || node.source || node.notes) && (
                 <div style={{
                   fontSize: '12px',
                   color: '#666',
@@ -116,7 +116,7 @@ export default function ListView({ nodes, onNodeClick }: ListViewProps) {
                   WebkitBoxOrient: 'vertical',
                   overflow: 'hidden'
                 }}>
-                  {node.description || truncateContent(node.notes)}
+                  {node.description || truncateContent(node.source || node.notes)}
                 </div>
               )}
 

src/config/skills/db-operations.md

@@ -1,9 +1,6 @@
 ---
 name: DB Operations
-description: "Use this for all graph read/write operations with strict data quality standards."
-when_to_use: "Any request to read, create, update, connect, classify, or traverse graph data."
-when_not_to_use: "Pure conversation with no graph interaction needed."
-success_criteria: "Writes are explicit and correct; descriptions are concrete; edges and dimensions are high-signal."
+description: "Use for graph read, write, connect, classify, or traverse operations with strict data quality standards."
 ---
 
 # DB Operations
@@ -20,8 +17,9 @@ success_criteria: "Writes are explicit and correct; descriptions are concrete; e
 
 - `title`: clear and specific.
 - `description`: concrete object-level description, not vague summaries.
-- `notes/content`: extra context, analysis, supporting detail.
+- `source`: full verbatim or canonical content of the node (transcript, article text, book passage, user's thoughts). This is what gets chunked and embedded for semantic search.
 - `link`: external source URL only.
+- Derived analysis, briefs, and research notes should be stored in a separate linked node, not appended to the source node.
 
 ## Execution Pattern
 

src/services/agents/quickAdd.ts

@@ -236,7 +236,7 @@ async function handleExtractionQuickAdd(type: ExtractionQuickAddType, url: strin
     const title = deriveFallbackLinkTitle(url);
     const description =
       `Link record for this source. RA-H could not correctly process the URL during ingestion because ${message}. Stored so the source is not lost and can be revisited later.`;
-    const notes = [
+    const source = [
       `Original URL: ${url}`,
       `Ingestion failure: ${message}`,
       `Attempted pipeline: ${type}`,
@@ -248,7 +248,7 @@ async function handleExtractionQuickAdd(type: ExtractionQuickAddType, url: strin
       body: JSON.stringify({
         title,
         description,
-        notes,
+        source,
         link: url,
         metadata: {
           source: 'quick-add-link-fallback',
@@ -292,7 +292,7 @@ async function handleNoteQuickAdd(rawInput: string, task: string, userDescriptio
   const title = deriveNoteTitle(content);
   const nodePayload: Record<string, unknown> = {
     title,
-    notes: content,
+    source: content,
     metadata: {
       source: 'quick-add-note',
       refined_at: new Date().toISOString(),
@@ -396,8 +396,8 @@ async function handleChatTranscriptQuickAdd(rawInput: string, task: string): Pro
     headers: { 'Content-Type': 'application/json' },
     body: JSON.stringify({
       title,
-      notes: content,
-      chunk: transcript,
+      source: transcript,
+      description: content,
       metadata,
     }),
   });

src/services/database/edges.ts

@@ -478,17 +478,13 @@ export class EdgeService {
           ELSE n_from.title
         END as connected_node_title,
         CASE
-          WHEN e.from_node_id = ? THEN n_to.notes
-          ELSE n_from.notes
-        END as connected_node_notes,
-        CASE 
           WHEN e.from_node_id = ? THEN n_to.link
           ELSE n_from.link
         END as connected_node_link,
         CASE 
-          WHEN e.from_node_id = ? THEN n_to.chunk
-          ELSE n_from.chunk
-        END as connected_node_chunk,
+          WHEN e.from_node_id = ? THEN n_to.source
+          ELSE n_from.source
+        END as connected_node_source,
         CASE 
           WHEN e.from_node_id = ? THEN n_to.metadata
           ELSE n_from.metadata
@@ -547,11 +543,10 @@ export class EdgeService {
       const connected_node: Node = {
         id: row.connected_node_id,
         title: row.connected_node_title,
-        notes: row.connected_node_notes,
         link: row.connected_node_link,
         dimensions: row.connected_node_dimensions,
         embedding: undefined, // Not needed for display
-        chunk: row.connected_node_chunk,
+        source: row.connected_node_source,
         metadata: row.connected_node_metadata,
         created_at: row.connected_node_created_at,
         updated_at: row.connected_node_updated_at
@@ -592,11 +587,10 @@ export class EdgeService {
       const connected_node: Node = {
         id: row.connected_node_id,
         title: row.connected_node_title,
-        notes: row.connected_node_notes,
         link: row.connected_node_link,
         dimensions: JSON.parse(row.connected_node_dimensions_json || '[]'),
         embedding: undefined, // Not needed for display
-        chunk: row.connected_node_chunk,
+        source: row.connected_node_source,
         metadata: typeof row.connected_node_metadata === 'string' ? JSON.parse(row.connected_node_metadata) : row.connected_node_metadata,
         created_at: row.connected_node_created_at,
         updated_at: row.connected_node_updated_at

src/services/database/nodes.ts

@@ -16,6 +16,38 @@ function sanitizeFtsQuery(input: string): string {
     .join(' ');
 }
 
+function extractRelaxedSearchTerms(query: string): string[] {
+  const stopWords = new Set([
+    'a', 'an', 'and', 'are', 'as', 'at', 'be', 'by', 'can', 'do', 'find',
+    'for', 'from', 'hello', 'i', 'in', 'is', 'it', 'me', 'my', 'of', 'on',
+    'or', 'recent', 'stuff', 'term', 'that', 'the', 'this', 'to', 'with', 'you'
+  ]);
+
+  const rawTerms = query
+    .toLowerCase()
+    .replace(/[^a-z0-9\s]+/g, ' ')
+    .split(/\s+/)
+    .map(term => term.trim())
+    .filter(Boolean);
+
+  const expanded = new Set<string>();
+
+  for (const term of rawTerms) {
+    if (!stopWords.has(term) && term.length >= 3) {
+      expanded.add(term);
+    }
+
+    const alphaParts = term.replace(/\d+/g, ' ').split(/\s+/).filter(Boolean);
+    for (const part of alphaParts) {
+      if (!stopWords.has(part) && part.length >= 3) {
+        expanded.add(part);
+      }
+    }
+  }
+
+  return Array.from(expanded).slice(0, 8);
+}
+
 function reciprocalRankFuse<T extends { id: number }>(
   rankedLists: T[][],
   limit: number,
@@ -48,7 +80,7 @@ export class NodeService {
 
   async countNodes(filters: NodeFilters = {}): Promise<number> {
     const { dimensions, search, dimensionsMatch = 'any',
-            createdAfter, createdBefore, eventAfter, eventBefore } = filters;
+            createdAfter, createdBefore, eventAfter, eventBefore, chunkStatus } = filters;
 
     if (search?.trim()) {
       return this.countSearchNodesSQLite(filters);
@@ -78,7 +110,7 @@ export class NodeService {
     }
 
     if (search) {
-      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
       params.push(`%${search}%`, `%${search}%`, `%${search}%`);
     }
 
@@ -86,6 +118,7 @@ export class NodeService {
     if (createdBefore) { query += ` AND n.created_at < ?`; params.push(createdBefore); }
     if (eventAfter) { query += ` AND n.event_date >= ?`; params.push(eventAfter); }
     if (eventBefore) { query += ` AND n.event_date < ?`; params.push(eventBefore); }
+    if (chunkStatus) { query += ` AND n.chunk_status = ?`; params.push(chunkStatus); }
 
     const result = sqlite.query<{ total: number }>(query, params);
     return result.rows[0]?.total ?? 0;
@@ -95,7 +128,7 @@ export class NodeService {
 
   private async getNodesSQLite(filters: NodeFilters = {}): Promise<Node[]> {
     const { dimensions, search, limit = 100, offset = 0, sortBy, dimensionsMatch = 'any',
-            createdAfter, createdBefore, eventAfter, eventBefore } = filters;
+            createdAfter, createdBefore, eventAfter, eventBefore, chunkStatus } = filters;
 
     if (search?.trim()) {
       return this.searchNodesSQLite(filters);
@@ -105,7 +138,7 @@ export class NodeService {
     
     // Use nodes_v view for array-like dimensions behavior (exclude embedding BLOB for performance)
     let query = `
-      SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+      SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
              n.chunk_status, n.embedding_updated_at, n.embedding_text,
              n.created_at, n.updated_at,
              COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
@@ -137,9 +170,9 @@ export class NodeService {
       }
     }
 
-    // Text search in title, description, and notes (SQLite LIKE with COLLATE NOCASE)
+    // Text search in title, description, and source (SQLite LIKE with COLLATE NOCASE)
     if (search) {
-      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
       params.push(`%${search}%`, `%${search}%`, `%${search}%`);
     }
 
@@ -160,23 +193,27 @@ export class NodeService {
       query += ` AND n.event_date < ?`;
       params.push(eventBefore);
     }
+    if (chunkStatus) {
+      query += ` AND n.chunk_status = ?`;
+      params.push(chunkStatus);
+    }
 
     // Sorting logic
     if (search) {
-      // For search queries, prioritize by relevance: exact title → starts with → contains in title → description → notes
+      // For search queries, prioritize by relevance: exact title → starts with → contains in title → description → source
       query += ` ORDER BY
         CASE WHEN LOWER(n.title) = LOWER(?) THEN 1 ELSE 6 END,
         CASE WHEN LOWER(n.title) LIKE LOWER(?) THEN 2 ELSE 6 END,
         CASE WHEN n.title LIKE ? COLLATE NOCASE THEN 3 ELSE 6 END,
         CASE WHEN n.description LIKE ? COLLATE NOCASE THEN 4 ELSE 6 END,
-        CASE WHEN n.notes LIKE ? COLLATE NOCASE THEN 5 ELSE 6 END,
+        CASE WHEN n.source LIKE ? COLLATE NOCASE THEN 5 ELSE 6 END,
         n.updated_at DESC`;
       params.push(
         search,           // Exact match (case-insensitive)
         `${search}%`,     // Starts with search term
         `%${search}%`,    // Contains in title
         `%${search}%`,    // Contains in description
-        `%${search}%`     // Contains in notes
+        `%${search}%`     // Contains in source
       );
     } else if (sortBy === 'edges') {
       // Sort by edge count (most connected first)
@@ -215,7 +252,7 @@ export class NodeService {
   private async getNodeByIdSQLite(id: number): Promise<Node | null> {
     const sqlite = getSQLiteClient();
     const query = `
-      SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+      SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
              n.chunk_status, n.embedding_updated_at, n.embedding_text,
              n.created_at, n.updated_at,
              COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension) 
@@ -241,11 +278,10 @@ export class NodeService {
     const {
       title,
       description,
-      notes,
+      source,
       link,
       event_date,
       dimensions = [],
-      chunk,
       chunk_status,
       metadata = {}
     } = nodeData;
@@ -255,16 +291,15 @@ export class NodeService {
     const nodeId = sqlite.transaction(() => {
       // Insert node using prepare/run for lastInsertRowid access
       const nodeResult = sqlite.prepare(`
-        INSERT INTO nodes (title, description, notes, link, event_date, metadata, chunk, chunk_status, created_at, updated_at)
-        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        INSERT INTO nodes (title, description, source, link, event_date, metadata, chunk_status, created_at, updated_at)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
       `).run(
         title,
         description ?? null,
-        notes ?? null,
+        source ?? null,
         link ?? null,
         event_date ?? null,
         JSON.stringify(metadata),
-        chunk ?? null,
         chunk_status ?? null,
         now,
         now
@@ -308,7 +343,7 @@ export class NodeService {
   // PostgreSQL path removed in SQLite-only consolidation
 
   private async updateNodeSQLite(id: number, updates: Partial<Node>): Promise<Node> {
-    const { title, description, notes, link, event_date, dimensions, chunk, metadata } = updates;
+    const { title, description, source, link, event_date, dimensions, metadata } = updates;
     const now = new Date().toISOString();
     const sqlite = getSQLiteClient();
 
@@ -327,10 +362,9 @@ export class NodeService {
       
       if (title !== undefined) { setFields.push('title = ?'); params.push(title); }
       if (description !== undefined) { setFields.push('description = ?'); params.push(description); }
-      if (notes !== undefined) { setFields.push('notes = ?'); params.push(notes); }
+      if (source !== undefined) { setFields.push('source = ?'); params.push(source); }
       if (link !== undefined) { setFields.push('link = ?'); params.push(link); }
       if (event_date !== undefined) { setFields.push('event_date = ?'); params.push(event_date); }
-      if (chunk !== undefined) { setFields.push('chunk = ?'); params.push(chunk); }
       if (Object.prototype.hasOwnProperty.call(updates, 'chunk_status')) {
         setFields.push('chunk_status = ?');
         params.push(updates.chunk_status ?? null);
@@ -469,6 +503,10 @@ export class NodeService {
       rankedRows = this.searchNodesLike(sqlite, search, filters, searchLimit);
     }
 
+    if (rankedRows.length === 0) {
+      rankedRows = this.searchNodesLikeRelaxed(sqlite, search, filters, searchLimit);
+    }
+
     if ((filters.searchMode ?? 'standard') === 'hybrid') {
       const vectorRows = await this.searchNodesVector(sqlite, search, filters, searchLimit);
       if (vectorRows.length > 0) {
@@ -518,7 +556,7 @@ export class NodeService {
     }
 
     for (const word of words) {
-      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
       queryParams.push(`%${word}%`, `%${word}%`, `%${word}%`);
     }
 
@@ -551,7 +589,7 @@ export class NodeService {
           WHERE nodes_fts MATCH ?
           LIMIT ?
         )
-        SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+        SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
                n.chunk_status, n.embedding_updated_at, n.embedding_text,
                n.created_at, n.updated_at,
                COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
@@ -580,7 +618,7 @@ export class NodeService {
     const words = search.split(/\s+/).filter(Boolean);
     const { clauses, params } = this.buildNodeFilterClauses(filters);
     let query = `
-      SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+      SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
              n.chunk_status, n.embedding_updated_at, n.embedding_text,
              n.created_at, n.updated_at,
              COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
@@ -595,7 +633,7 @@ export class NodeService {
     }
 
     for (const word of words) {
-      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.notes LIKE ? COLLATE NOCASE)`;
+      query += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.source LIKE ? COLLATE NOCASE)`;
       queryParams.push(`%${word}%`, `%${word}%`, `%${word}%`);
     }
 
@@ -604,7 +642,7 @@ export class NodeService {
       CASE WHEN LOWER(n.title) LIKE LOWER(?) THEN 2 ELSE 6 END,
       CASE WHEN n.title LIKE ? COLLATE NOCASE THEN 3 ELSE 6 END,
       CASE WHEN n.description LIKE ? COLLATE NOCASE THEN 4 ELSE 6 END,
-      CASE WHEN n.notes LIKE ? COLLATE NOCASE THEN 5 ELSE 6 END,
+      CASE WHEN n.source LIKE ? COLLATE NOCASE THEN 5 ELSE 6 END,
       n.updated_at DESC
       LIMIT ?`;
 
@@ -614,6 +652,62 @@ export class NodeService {
     return result.rows;
   }
 
+  private searchNodesLikeRelaxed(
+    sqlite: ReturnType<typeof getSQLiteClient>,
+    search: string,
+    filters: NodeFilters,
+    limit: number,
+  ): NodeSearchRow[] {
+    const terms = extractRelaxedSearchTerms(search);
+    if (terms.length === 0) return [];
+
+    const { clauses, params } = this.buildNodeFilterClauses(filters);
+    let query = `
+      SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+             n.chunk_status, n.embedding_updated_at, n.embedding_text,
+             n.created_at, n.updated_at,
+             COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
+                       FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
+      FROM nodes n
+      WHERE 1=1
+    `;
+    const queryParams = [...params];
+
+    if (clauses.length > 0) {
+      query += ` AND ${clauses.join(' AND ')}`;
+    }
+
+    const termClauses: string[] = [];
+    for (const term of terms) {
+      termClauses.push(`n.title LIKE ? COLLATE NOCASE`);
+      termClauses.push(`n.description LIKE ? COLLATE NOCASE`);
+      termClauses.push(`n.source LIKE ? COLLATE NOCASE`);
+      queryParams.push(`%${term}%`, `%${term}%`, `%${term}%`);
+    }
+
+    query += ` AND (${termClauses.join(' OR ')})`;
+
+    const scoreClauses: string[] = [];
+    const scoreParams: string[] = [];
+    for (const term of terms) {
+      scoreClauses.push(`CASE WHEN n.title LIKE ? COLLATE NOCASE THEN 3 ELSE 0 END`);
+      scoreClauses.push(`CASE WHEN n.description LIKE ? COLLATE NOCASE THEN 2 ELSE 0 END`);
+      scoreClauses.push(`CASE WHEN n.source LIKE ? COLLATE NOCASE THEN 1 ELSE 0 END`);
+      scoreParams.push(`%${term}%`, `%${term}%`, `%${term}%`);
+    }
+
+    query += ` ORDER BY
+      (${scoreClauses.join(' + ')}) DESC,
+      CASE WHEN LOWER(n.title) LIKE LOWER(?) THEN 0 ELSE 1 END,
+      n.updated_at DESC
+      LIMIT ?`;
+
+    queryParams.push(...scoreParams, `%${search}%`, limit);
+
+    const result = sqlite.query<NodeSearchRow>(query, queryParams);
+    return result.rows;
+  }
+
   private async searchNodesVector(
     sqlite: ReturnType<typeof getSQLiteClient>,
     search: string,
@@ -643,7 +737,7 @@ export class NodeService {
           ORDER BY distance
           LIMIT ?
         )
-        SELECT n.id, n.title, n.description, n.notes, n.link, n.event_date, n.metadata, n.chunk,
+        SELECT n.id, n.title, n.description, n.source, n.notes, n.link, n.event_date, n.metadata, n.chunk,
                n.chunk_status, n.embedding_updated_at, n.embedding_text,
                n.created_at, n.updated_at,
                COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)

src/services/database/sqlite-client.ts

@@ -616,13 +616,60 @@ class SQLiteClient {
 
       // 10) Final schema pass migrations (content→notes, event_date, dimensions.icon, drop dead columns)
       try {
-        const nodeCols2 = this.db.prepare('PRAGMA table_info(nodes)').all() as Array<{ name: string }>;
-        const nodeColNames = nodeCols2.map(c => c.name);
+        let nodeCols2 = this.db.prepare('PRAGMA table_info(nodes)').all() as Array<{ name: string }>;
+        let nodeColNames = nodeCols2.map(c => c.name);
 
         // Rename content → notes (additive first)
         if (nodeColNames.includes('content') && !nodeColNames.includes('notes')) {
           console.log('Migrating nodes.content → nodes.notes...');
           this.db.exec('ALTER TABLE nodes RENAME COLUMN content TO notes;');
+          nodeCols2 = this.db.prepare('PRAGMA table_info(nodes)').all() as Array<{ name: string }>;
+          nodeColNames = nodeCols2.map(c => c.name);
+        }
+
+        if (!nodeColNames.includes('source')) {
+          console.log('Adding nodes.source column...');
+          this.db.exec('ALTER TABLE nodes ADD COLUMN source TEXT;');
+          nodeCols2 = this.db.prepare('PRAGMA table_info(nodes)').all() as Array<{ name: string }>;
+          nodeColNames = nodeCols2.map(c => c.name);
+        }
+
+        if (nodeColNames.includes('source')) {
+          this.db.exec(`
+            UPDATE nodes
+            SET source = chunk
+            WHERE (source IS NULL OR LENGTH(TRIM(source)) = 0)
+              AND chunk IS NOT NULL
+              AND LENGTH(TRIM(chunk)) > 0;
+          `);
+
+          this.db.exec(`
+            UPDATE nodes
+            SET source = notes,
+                chunk_status = 'not_chunked'
+            WHERE (source IS NULL OR LENGTH(TRIM(source)) = 0)
+              AND notes IS NOT NULL
+              AND LENGTH(TRIM(notes)) > 0;
+          `);
+
+          this.db.exec(`
+            UPDATE nodes
+            SET source = title || CASE
+              WHEN description IS NOT NULL AND LENGTH(TRIM(description)) > 0
+                THEN char(10) || char(10) || description
+              ELSE ''
+            END,
+            chunk_status = 'not_chunked'
+            WHERE source IS NULL OR LENGTH(TRIM(source)) = 0;
+          `);
+
+          this.db.exec(`
+            UPDATE nodes
+            SET chunk_status = 'not_chunked'
+            WHERE source IS NOT NULL
+              AND LENGTH(TRIM(source)) > 0
+              AND (chunk_status IS NULL OR chunk_status != 'chunked');
+          `);
         }
 
         // Add event_date
@@ -657,8 +704,10 @@ class SQLiteClient {
         if (edgeCols.some(c => c.name === 'user_feedback')) {
           try { this.db.exec('ALTER TABLE edges DROP COLUMN user_feedback;'); } catch {}
         }
+        // edges.explanation (top-level column added alongside context JSON)
         if (!edgeCols.some(c => c.name === 'explanation')) {
           this.db.exec('ALTER TABLE edges ADD COLUMN explanation TEXT;');
+          // Backfill from context JSON where available
           try {
             this.db.exec(`
               UPDATE edges SET explanation = json_extract(context, '$.explanation')
@@ -667,13 +716,13 @@ class SQLiteClient {
           } catch {}
         }
 
-        // Recreate nodes_fts to index title + description + notes
+        // Recreate nodes_fts to index title + source + description
         try {
           const ftsCheck = this.db.prepare("SELECT sql FROM sqlite_master WHERE name='nodes_fts'").get() as { sql?: string } | undefined;
-          if (ftsCheck?.sql && (!ftsCheck.sql.includes('description') || ftsCheck.sql.includes('content'))) {
+          const needsRebuild = !ftsCheck?.sql || !ftsCheck.sql.includes('source') || ftsCheck.sql.includes('notes') || ftsCheck.sql.includes('content');
+          if (needsRebuild) {
             this.db.exec('DROP TABLE IF EXISTS nodes_fts;');
-            this.db.exec("CREATE VIRTUAL TABLE nodes_fts USING fts5(title, description, notes, content='nodes', content_rowid='id');");
-            // Rebuild FTS index
+            this.db.exec("CREATE VIRTUAL TABLE nodes_fts USING fts5(title, source, description, content='nodes', content_rowid='id');");
             this.db.exec("INSERT INTO nodes_fts(nodes_fts) VALUES('rebuild');");
           }
         } catch (ftsErr) {

src/services/embedding/autoEmbedQueue.ts

@@ -16,12 +16,15 @@ export class AutoEmbedQueue {
   private readonly lastRunAt = new Map<number, number>();
   private readonly maxConcurrent = 1;
   private readonly cooldownMs = DEFAULT_COOLDOWN_MS;
-  private readonly embeddingsDisabled = process.env.DISABLE_EMBEDDINGS === 'true';
+
+  async recoverStuckNodes(): Promise<void> {
+    const stuckNodes = await nodeService.getNodes({ chunkStatus: 'not_chunked', limit: 1000 });
+    for (const node of stuckNodes) {
+      this.enqueue(node.id, { reason: 'startup_recovery' });
+    }
+  }
 
   enqueue(nodeId: number, task: Omit<AutoEmbedTask, 'nodeId'> = {}): boolean {
-    if (this.embeddingsDisabled && !task.force) {
-      return false;
-    }
     const existing = this.pendingTasks.get(nodeId);
     if (!existing) {
       this.pendingTasks.set(nodeId, { nodeId, ...task });
@@ -77,21 +80,12 @@ export class AutoEmbedQueue {
   }
 
   private async executeTask(task: AutoEmbedTask) {
-    if (this.embeddingsDisabled && !task.force) {
-      return;
-    }
     const node = await nodeService.getNodeById(task.nodeId);
     if (!node) {
       console.warn('[AutoEmbedQueue] Node missing, skipping', task.nodeId);
       return;
     }
 
-    const chunkText = node.chunk?.trim();
-    if (!chunkText) {
-      console.warn('[AutoEmbedQueue] Node has no chunk content, skipping', task.nodeId);
-      return;
-    }
-
     if (!task.force && node.chunk_status === 'chunked') {
       return;
     }
@@ -117,4 +111,7 @@ declare global {
 export const autoEmbedQueue = globalThis.autoEmbedQueue ?? new AutoEmbedQueue();
 if (!globalThis.autoEmbedQueue) {
   globalThis.autoEmbedQueue = autoEmbedQueue;
+  autoEmbedQueue.recoverStuckNodes().catch(error => {
+    console.error('[AutoEmbedQueue] Startup recovery failed', error);
+  });
 }

src/services/embedding/ingestion.ts

@@ -103,10 +103,10 @@ export async function embedNodeContent(nodeId: number): Promise<EmbeddingPipelin
     };
   }
 
-  if (!node.chunk || !node.chunk.trim()) {
+  if (!node.source || !node.source.trim()) {
     results.chunk_embeddings = {
       status: 'skipped',
-      message: 'No chunk content to embed',
+      message: 'No source content to embed',
       chunks_created: 0
     };
   } else {

src/services/typescript/embed-nodes.ts

@@ -16,6 +16,7 @@ import {
 interface NodeRecord {
   id: number;
   title: string;
+  source: string | null;
   notes: string | null;
   description: string | null;
   dimensions_json: string;
@@ -58,7 +59,7 @@ export class NodeEmbedder {
     const prompt = `Analyze this content and provide 2-3 key insights or themes in a concise paragraph (max 100 words):
 
 Title: ${node.title}
-Content: ${node.notes || 'No content'}
+Source: ${node.source || node.notes || 'No source'}
 Dimensions: ${dimensionsText}
 
 Focus on the main concepts, key relationships, and practical implications.`;
@@ -106,13 +107,14 @@ Focus on the main concepts, key relationships, and practical implications.`;
     // Create base embedding text
     let embeddingText = formatEmbeddingText(
       node.title,
-      node.notes || '',
+      node.source || node.notes || '',
       dimensions,
       node.description
     );
 
-    // Add AI analysis if content exists
-    if (node.notes && node.notes.trim().length > 0) {
+    // Add AI analysis if source exists
+    const sourceText = node.source || node.notes || '';
+    if (sourceText.trim().length > 0) {
       const analysis = await this.analyzeNodeWithAI(node);
       if (analysis) {
         embeddingText += `\n\nAI Analysis: ${analysis}`;
@@ -176,8 +178,8 @@ Focus on the main concepts, key relationships, and practical implications.`;
     
     if (nodeId) {
       // Single node
-      query = `
-        SELECT n.id, n.title, n.content, n.description,
+        query = `
+        SELECT n.id, n.title, n.source, n.notes, n.description,
                COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                         FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json,
                n.embedding, n.embedding_updated_at
@@ -188,7 +190,7 @@ Focus on the main concepts, key relationships, and practical implications.`;
     } else if (forceReEmbed) {
       // All nodes
       query = `
-        SELECT n.id, n.title, n.content, n.description,
+        SELECT n.id, n.title, n.source, n.notes, n.description,
                COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                         FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json,
                n.embedding, n.embedding_updated_at
@@ -198,7 +200,7 @@ Focus on the main concepts, key relationships, and practical implications.`;
     } else {
       // Only nodes without embeddings
       query = `
-        SELECT n.id, n.title, n.content, n.description,
+        SELECT n.id, n.title, n.source, n.notes, n.description,
                COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                         FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json,
                n.embedding, n.embedding_updated_at

src/services/typescript/embed-universal.ts

@@ -1,6 +1,6 @@
 /**
  * Universal chunking and embedding service for RA-H knowledge management system
- * Takes a node_id, reads chunk content from nodes table, chunks it, and stores in chunks table
+ * Takes a node_id, reads source content from nodes table, chunks it, and stores in chunks table
  */
 
 import OpenAI from 'openai';
@@ -14,7 +14,7 @@ import {
 interface Node {
   id: number;
   title: string;
-  chunk: string | null;
+  source: string | null;
   chunk_status?: string | null;
 }
 
@@ -157,7 +157,7 @@ export class UniversalEmbedder {
     
     // Get node data
     const stmt = this.db.prepare(`
-      SELECT id, title, chunk, chunk_status
+      SELECT id, title, source, chunk_status
       FROM nodes
       WHERE id = ?
     `);
@@ -168,8 +168,8 @@ export class UniversalEmbedder {
       throw new Error(`Node ${nodeId} not found`);
     }
     
-    if (!node.chunk || node.chunk.trim().length === 0) {
-      console.log(`Node ${nodeId} has no chunk content to process`);
+    if (!node.source || node.source.trim().length === 0) {
+      console.log(`Node ${nodeId} has no source content to process`);
       return { chunks: 0 };
     }
     
@@ -179,7 +179,7 @@ export class UniversalEmbedder {
     this.deleteExistingChunks(nodeId);
     
     // Split text into chunks
-    const chunks = await this.textSplitter.splitText(node.chunk);
+    const chunks = await this.textSplitter.splitText(node.source);
     
     if (verbose) {
       console.log(`Split into ${chunks.length} chunks`);

src/tools/database/createNode.ts

@@ -8,8 +8,8 @@ export const createNodeTool = tool({
   description: 'Create node. Description is REQUIRED and must be explicit about what the thing is (podcast, chat summary, idea, etc).',
   inputSchema: z.object({
     title: z.string().describe('The title of the node'),
-    notes: z.string().optional().describe('User notes, analysis, or thoughts about this node'),
     description: z.string().max(280).describe('REQUIRED. Explicitly state WHAT this is (e.g. podcast episode, conversation summary, user insight) + WHY it matters for context grounding.'),
+    source: z.string().optional().describe('Raw content for embedding: transcript, article text, book passages, or user thoughts. If omitted, falls back to title + description.'),
     link: z.string().optional().describe('A URL link to the source'),
     event_date: z.string().optional().describe('When the thing actually happened (ISO 8601). Not when it was added to the graph.'),
     dimensions: z
@@ -17,7 +17,6 @@ export const createNodeTool = tool({
       .max(5)
       .optional()
       .describe('Optional dimension tags to apply to this node (0-5 items).'),
-    chunk: z.string().optional().describe('Raw content for later processing - CRITICAL for extracted content from URLs'),
     metadata: z.record(z.any()).optional().describe('Additional metadata like source info, extraction details, etc.')
   }),
   execute: async (params) => {

src/tools/database/getNodesById.ts

@@ -6,9 +6,9 @@ export const getNodesByIdTool = tool({
   description: 'Load full node records by IDs',
   inputSchema: z.object({
     nodeIds: z.array(z.number().int().positive()).min(1).max(10).describe('List of node IDs to load'),
-    includeNotesPreview: z.boolean().default(true).describe('Whether to return a trimmed content preview for each node'),
+    includeSourcePreview: z.boolean().default(true).describe('Whether to return a trimmed source preview for each node'),
   }),
-  execute: async ({ nodeIds, includeNotesPreview }) => {
+  execute: async ({ nodeIds, includeSourcePreview }) => {
     const uniqueIds = Array.from(new Set(nodeIds.filter(id => Number.isFinite(id) && id > 0)));
     if (uniqueIds.length === 0) {
       return {
@@ -23,8 +23,8 @@ export const getNodesByIdTool = tool({
         try {
           const node = await nodeService.getNodeById(id);
           if (!node) return null;
-          const preview = includeNotesPreview
-            ? (node.notes || node.description || '')
+          const preview = includeSourcePreview
+            ? (node.source || node.description || '')
                 .split(/\s+/)
                 .slice(0, 80)
                 .join(' ')
@@ -35,10 +35,12 @@ export const getNodesByIdTool = tool({
             id: node.id,
             title: node.title,
             link: node.link,
+            event_date: node.event_date ?? null,
             dimensions: node.dimensions || [],
             chunk_status: node.chunk_status || 'unknown',
+            created_at: node.created_at,
             updated_at: node.updated_at,
-            notes_preview: preview || null,
+            source_preview: preview || null,
             metadata: node.metadata ?? null,
           };
         } catch (error) {

src/tools/database/queryDimensionNodes.ts

@@ -48,11 +48,12 @@ export const queryDimensionNodesTool = tool({
           event_date: node.event_date ?? null,
         };
 
-        if (includeContent && node.notes) {
+        if (includeContent && (node.source || node.notes)) {
+          const previewSource = node.source || node.notes || '';
           // Truncate to ~100 chars
-          formatted.notesPreview = node.notes.length > 100
-            ? node.notes.substring(0, 100) + '...'
-            : node.notes;
+          formatted.sourcePreview = previewSource.length > 100
+            ? previewSource.substring(0, 100) + '...'
+            : previewSource;
         }
 
         return formatted;

src/tools/database/queryNodes.ts

@@ -44,7 +44,7 @@ function scoreNodeForSearch(node: Node, searchTerm: string): number {
   const normalizedSearch = searchTerm.toLowerCase();
   const title = (node.title || '').toLowerCase();
   const description = (node.description || '').toLowerCase();
-  const notes = (node.notes || '').toLowerCase();
+  const source = (node.source || '').toLowerCase();
   const terms = extractSearchTerms(searchTerm);
 
   let score = 0;
@@ -52,23 +52,23 @@ function scoreNodeForSearch(node: Node, searchTerm: string): number {
   if (title === normalizedSearch) score += 100;
   if (title.includes(normalizedSearch)) score += 40;
   if (description.includes(normalizedSearch)) score += 20;
-  if (notes.includes(normalizedSearch)) score += 10;
+  if (source.includes(normalizedSearch)) score += 10;
 
   for (const term of terms) {
     if (title.includes(term)) score += 8;
     if (description.includes(term)) score += 3;
-    if (notes.includes(term)) score += 2;
+    if (source.includes(term)) score += 2;
   }
 
   return score;
 }
 
 export const queryNodesTool = tool({
-  description: 'Search nodes across title, description, and notes. For free-text lookups, search the graph broadly and prioritize title/description matches. Do not use dimensions to constrain keyword search unless the user is explicitly asking about a known dimension.',
+  description: 'Search nodes across title, description, and source. For free-text lookups, search the graph broadly and prioritize title/description matches. Do not use dimensions to constrain keyword search unless the user is explicitly asking about a known dimension.',
   inputSchema: z.object({
     filters: z.object({
       dimensions: z.array(z.string()).describe('Filter by dimensions (e.g., ["research", "ai", "technology"]). Replaces old type/stage filtering.').optional(),
-      search: z.string().describe('Search term to match against node title, description, or notes').optional(),
+      search: z.string().describe('Search term to match against node title, description, or source').optional(),
       limit: z.number().min(1).max(50).default(10).describe('Maximum number of results to return'),
       createdAfter: z.string().optional().describe('ISO date (YYYY-MM-DD). Only return nodes created on or after this date.'),
       createdBefore: z.string().optional().describe('ISO date (YYYY-MM-DD). Only return nodes created before this date.'),

src/tools/database/updateNode.ts

@@ -9,14 +9,13 @@ export const updateNodeTool = tool({
     id: z.number().describe('The ID of the node to update'),
     updates: z.object({
       title: z.string().optional().describe('New title'),
-      notes: z.string().optional().describe('User notes/analysis to append. USE THIS for workflow outputs, briefs, research notes, etc.'),
       description: z.string().max(280).describe('REQUIRED on every update. Explicitly state WHAT this is + WHY it matters. No "discusses/explores".'),
+      source: z.string().optional().describe('Canonical source content for embedding. Use this only to set or correct the raw source text.'),
       link: z.string().optional().describe('New link'),
       event_date: z.string().optional().describe('When the thing actually happened (ISO 8601). Not when it was added to the graph.'),
       dimensions: z.array(z.string()).optional().describe('New dimension tags - completely replaces existing dimensions'),
-      chunk: z.string().optional().describe('DO NOT USE - raw source text that triggers re-embedding. Only for source corrections.'),
       metadata: z.record(z.any()).optional().describe('New metadata - completely replaces existing metadata')
-    }).describe('Object containing the fields to update. For adding notes/analysis, always use "notes" field.')
+    }).describe('Object containing the fields to update. Derived analysis should be stored in a separate linked node, not appended to the source node.')
   }),
   execute: async ({ id, updates }) => {
     try {
@@ -44,56 +43,6 @@ export const updateNodeTool = tool({
         };
       }
 
-      // FORCE APPEND for notes field - fetch existing and append new notes
-      if (updates.notes) {
-        const fetchResponse = await fetch(`${getInternalApiBaseUrl()}/api/nodes/${id}`);
-        if (fetchResponse.ok) {
-          const { node } = await fetchResponse.json();
-          const existingNotes = (node?.notes || '').trim();
-          const newNotes = updates.notes.trim();
-
-          // Skip if new notes are identical to existing (model sent duplicate)
-          if (existingNotes === newNotes) {
-            console.log(`[updateNode] ERROR - new notes identical to existing (${existingNotes.length} chars). Model should NOT call updateNode again.`);
-            return {
-              success: false,
-              error: 'Notes already up to date - do not call updateNode again. Move to next step.',
-              data: null
-            };
-          }
-
-          // Detect if adding a section that already exists (e.g., ## Integration Analysis)
-          const newSectionMatch = newNotes.match(/^##\s+(.+)$/m);
-          if (newSectionMatch && existingNotes) {
-            const sectionHeader = newSectionMatch[0]; // e.g., "## Integration Analysis"
-            if (existingNotes.includes(sectionHeader)) {
-              console.log(`[updateNode] ERROR - Section "${sectionHeader}" already exists in node`);
-              return {
-                success: false,
-                error: `Section "${sectionHeader}" already exists in this node. Cannot append duplicate section.`,
-                data: null
-              };
-            }
-          }
-
-          // Detect if model included existing notes + new notes
-          if (existingNotes && newNotes.startsWith(existingNotes)) {
-            // Extract only the new part
-            const actualNewNotes = newNotes.substring(existingNotes.length).trim();
-            console.log(`[updateNode] Model included existing notes - extracting new part only (${actualNewNotes.length} chars)`);
-            const separator = existingNotes.endsWith('\n\n') ? '' : '\n\n';
-            updates.notes = `${existingNotes}${separator}${actualNewNotes}`;
-          } else if (existingNotes) {
-            // Normal append
-            const separator = existingNotes.endsWith('\n\n') ? '' : '\n\n';
-            updates.notes = `${existingNotes}${separator}${newNotes}`;
-            console.log(`[updateNode] Appended notes: ${existingNotes.length} + ${newNotes.length} = ${updates.notes.length} chars`);
-          } else {
-            console.log(`[updateNode] No existing notes, using new notes as-is (${newNotes.length} chars)`);
-          }
-        }
-      }
-
       if (Array.isArray(updates.dimensions)) {
         updates.dimensions = normalizeDimensions(updates.dimensions, 5);
       }

src/tools/other/paperExtract.ts

@@ -69,7 +69,7 @@ Respond with ONLY valid JSON (no markdown, no code blocks):
 }
 
 export const paperExtractTool = tool({
-  description: 'Extract a PDF or research paper into a node with summary, metadata, and full-text chunk',
+  description: 'Extract a PDF or research paper into a node with summary, metadata, and full-text source',
   inputSchema: z.object({
     url: z.string().describe('The PDF URL to add to inbox'),
     title: z.string().optional().describe('Custom title (auto-generated if not provided)'),
@@ -95,14 +95,13 @@ export const paperExtractTool = tool({
         };
       }
 
-      let result: { success: boolean; notes?: string; chunk?: string; metadata?: any; error?: string };
+      let result: { success: boolean; source?: string; metadata?: any; error?: string };
       
       try {
         const extractionResult = await extractPaper(url);
         result = {
           success: true,
-          notes: extractionResult.content,
-          chunk: extractionResult.chunk,
+          source: extractionResult.chunk || extractionResult.content,
           metadata: {
             title: extractionResult.metadata.title,
             pages: extractionResult.metadata.pages,
@@ -119,7 +118,7 @@ export const paperExtractTool = tool({
         };
       }
 
-      if (!result.success || (!result.notes && !result.chunk)) {
+      if (!result.success || !result.source) {
         return {
           success: false,
           error: result.error || 'Failed to extract PDF content',
@@ -132,7 +131,7 @@ export const paperExtractTool = tool({
       // Step 2: AI Analysis for enhanced metadata
       const aiAnalysis = await analyzeContentWithAI(
         result.metadata?.title || `PDF: ${new URL(url).pathname.split('/').pop()?.replace('.pdf', '')}`, 
-        result.notes?.substring(0, 2000) || 'PDF document content', 
+        result.source.substring(0, 2000) || 'PDF document content', 
         'pdf'
       );
 
@@ -153,17 +152,16 @@ export const paperExtractTool = tool({
         body: JSON.stringify({
           title: nodeTitle,
           description: aiAnalysis?.nodeDescription,
-          notes: enhancedDescription,
+          source: result.source,
           link: url,
           dimensions: trimmedDimensions,
-          chunk: result.chunk || result.notes,
           metadata: {
             source: 'pdf',
             hostname: new URL(url).hostname,
             author: result.metadata?.author || result.metadata?.info?.Author,
             pages: result.metadata?.pages,
             file_size: result.metadata?.file_size,
-            content_length: (result.chunk || result.notes)?.length,
+            content_length: result.source.length,
             extraction_method: result.metadata?.extraction_method || 'python_pdfplumber',
             ai_analysis: aiAnalysis?.reasoning,
             enhanced_description: enhancedDescription,
@@ -197,7 +195,7 @@ export const paperExtractTool = tool({
         data: {
           nodeId: createResult.data?.id,
           title: nodeTitle,
-          contentLength: (result.chunk || result.notes || '').length,
+          contentLength: result.source.length,
           url: url,
           dimensions: actualDimensions
         }

src/tools/other/websiteExtract.ts

@@ -149,7 +149,7 @@ Respond with ONLY valid JSON (no markdown, no code blocks):
 }
 
 export const websiteExtractTool = tool({
-  description: 'Extract website content and metadata into a node with summary, tags, and raw chunk',
+  description: 'Extract website content and metadata into a node with summary, tags, and raw source text',
   inputSchema: z.object({
     url: z.string().describe('The website URL to add to knowledge base'),
     title: z.string().optional().describe('Custom title (auto-generated if not provided)'),
@@ -166,14 +166,13 @@ export const websiteExtractTool = tool({
         };
       }
 
-      let result: { success: boolean; notes?: string; chunk?: string; metadata?: any; error?: string };
+      let result: { success: boolean; source?: string; metadata?: any; error?: string };
       
       try {
         const extractionResult = await extractWebsite(url);
         result = {
           success: true,
-          notes: extractionResult.content,
-          chunk: extractionResult.chunk,
+          source: extractionResult.chunk || extractionResult.content,
           metadata: {
             title: extractionResult.metadata.title,
             author: extractionResult.metadata.author,
@@ -191,7 +190,7 @@ export const websiteExtractTool = tool({
         };
       }
 
-      if (!result.success || (!result.notes && !result.chunk)) {
+      if (!result.success || !result.source) {
         return {
           success: false,
           error: result.error || 'Failed to extract website content',
@@ -206,7 +205,7 @@ export const websiteExtractTool = tool({
       const contentType = inferWebsiteContentType(url);
       const aiAnalysis = await analyzeContentWithAI(
         result.metadata?.title || `Website: ${new URL(url).hostname}`, 
-        result.notes?.substring(0, 2000) || 'Website content', 
+        result.source.substring(0, 2000) || 'Website content', 
         contentType,
         existingDimensions
       );
@@ -231,17 +230,16 @@ export const websiteExtractTool = tool({
         body: JSON.stringify({
           title: nodeTitle,
           description: aiAnalysis?.nodeDescription,
-          notes: enhancedDescription,
+          source: result.source,
           link: url,
           event_date: result.metadata?.published_date || result.metadata?.date || null,
           dimensions: finalDimensions,
-          chunk: result.chunk || result.notes,
           metadata: {
             source: contentType,
             hostname: new URL(url).hostname,
             author: result.metadata?.author,
             published_date: result.metadata?.published_date || result.metadata?.date,
-            content_length: (result.chunk || result.notes)?.length,
+            content_length: result.source.length,
             extraction_method: result.metadata?.extraction_method || 'python_beautifulsoup',
             ai_analysis: aiAnalysis?.reasoning,
             enhanced_description: enhancedDescription,
@@ -275,7 +273,7 @@ export const websiteExtractTool = tool({
         data: {
           nodeId: createResult.data?.id,
           title: nodeTitle,
-          contentLength: (result.chunk || result.notes || '').length,
+          contentLength: result.source.length,
           url: url,
           dimensions: actualDimensions
         }

src/tools/other/youtubeExtract.ts

@@ -193,15 +193,14 @@ export const youtubeExtractTool = tool({
         };
       }
 
-      let result: { success: boolean; notes?: string; chunk?: string; metadata?: any; error?: string };
+      let result: { success: boolean; source?: string; metadata?: any; error?: string };
       
       console.log('📝 Using TypeScript yt-dlp extractor');
       try {
         const extractionResult = await extractYouTube(url);
         result = {
           success: extractionResult.success,
-          notes: extractionResult.content,
-          chunk: extractionResult.chunk,
+          source: extractionResult.chunk || extractionResult.content,
           metadata: {
             video_title: extractionResult.metadata.video_title,
             channel_name: extractionResult.metadata.channel_name,
@@ -222,7 +221,7 @@ export const youtubeExtractTool = tool({
         };
       }
 
-      if (!result.success || (!result.notes && !result.chunk)) {
+      if (!result.success || !result.source) {
         return {
           success: false,
           error: result.error || 'Failed to extract YouTube content',
@@ -243,8 +242,7 @@ export const youtubeExtractTool = tool({
 
       // Step 3: Create node with extracted content and AI analysis
       const nodeTitle = title || result.metadata?.video_title || `YouTube Video ${url.split('/').pop()?.split('?')[0]}`;
-      const transcriptSummary = await summariseTranscript(nodeTitle, result.chunk || result.notes || '');
-      const nodeNotes = transcriptSummary || aiAnalysis?.enhancedDescription || `YouTube video by ${result.metadata?.channel_name || 'Unknown Channel'}`;
+      const transcriptSummary = await summariseTranscript(nodeTitle, result.source);
 
       const suppliedDimensions = Array.isArray(dimensions) ? dimensions : [];
       let trimmedDimensions = suppliedDimensions
@@ -262,10 +260,9 @@ export const youtubeExtractTool = tool({
         body: JSON.stringify({
           title: nodeTitle,
           description: aiAnalysis?.nodeDescription,
-          notes: nodeNotes,
+          source: result.source,
           link: url,
           dimensions: finalDimensions,
-          chunk: result.chunk || result.notes,
           metadata: {
             source: 'youtube',
             video_id: result.metadata?.video_id,
@@ -308,7 +305,7 @@ export const youtubeExtractTool = tool({
         data: {
           nodeId: createResult.data?.id,
           title: nodeTitle,
-          contentLength: (result.chunk || result.notes || '').length,
+          contentLength: result.source.length,
           url: url,
           dimensions: actualDimensions
         }

src/types/database.ts

@@ -3,12 +3,13 @@ export interface Node {
   id: number;
   title: string;
   description?: string;
-  notes?: string;             // User's notes/thoughts about this node
+  source?: string;            // Canonical embeddable content
+  notes?: string;             // Deprecated legacy field - do not write
   link?: string;
   event_date?: string | null; // When the thing actually happened (ISO 8601)
   dimensions: string[];       // Flexible dimensions replacing type + stage + segment + tags
   embedding?: Buffer;         // Node-level embedding (BLOB data)
-  chunk?: string;
+  chunk?: string;             // Deprecated legacy field - do not write
   metadata?: any;            // Flexible metadata storage
   created_at: string;
   updated_at: string;
@@ -68,6 +69,7 @@ export interface NodeFilters {
   dimensions?: string[];      // Filter by dimensions (replaces stage/type filtering)
   search?: string;           // Text search in title/content
   searchMode?: 'standard' | 'hybrid'; // standard = FTS/LIKE, hybrid = add node-vector retrieval
+  chunkStatus?: 'not_chunked' | 'chunking' | 'chunked' | 'error';
   limit?: number;
   offset?: number;
   sortBy?: 'updated' | 'edges' | 'created' | 'event_date';  // Sort by updated_at, edge count, created_at, or event_date