ra-h-os/apps/mcp-server-standalone/index.js

#!/usr/bin/env node
'use strict';

const { z } = require('zod');
const { McpServer } = require('@modelcontextprotocol/sdk/server/mcp.js');
const { StdioServerTransport } = require('@modelcontextprotocol/sdk/server/stdio.js');

const { initDatabase, getDatabasePath, closeDatabase, getDb, query } = require('./services/sqlite-client');
const nodeService = require('./services/nodeService');
const edgeService = require('./services/edgeService');
const dimensionService = require('./services/dimensionService');
const guideService = require('./services/guideService');

// Server info
const serverInfo = {
  name: 'ra-h-standalone',
  version: '1.4.0'
};

const instructions = [
  "RA-H is the user's personal knowledge graph — local SQLite, fully on-device.",
  'Call rah_get_context first for a quick orientation (stats, hubs, dimensions).',
  'For simple tasks (add a node, search), the tool descriptions have everything you need — just execute.',
  'For complex or ambiguous tasks, also call rah_read_guide("start-here") for full graph understanding.',
  'Knowledge capture: after substantive exchanges, offer to save valuable information.',
  'Triggers: a new insight emerges, a decision is made, a person/entity/concept is discussed in depth, research or references are shared, a connection to existing knowledge surfaces.',
  'When offering, propose a specific node — title, dimensions, one-line description — so the user can approve with minimal friction.',
  'Don\'t ask "should I save this?" — instead say "I\'d add this as: [title] in [dimensions] — want me to?"',
  'Search before creating to avoid duplicates.',
  'All data stays on this device.'
].join(' ');

// 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'),
  link: z.string().url().optional().describe('Source URL'),
  description: z.string().max(2000).optional().describe('One-sentence summary. Helps search and AI understanding.'),
  dimensions: z.array(z.string()).min(1).max(5).describe('1-5 categories. Call rah_list_dimensions first to use existing ones.'),
  metadata: z.record(z.any()).optional().describe('Additional metadata'),
  chunk: z.string().max(50000).optional().describe('Full source text')
};

const searchNodesInputSchema = {
  query: z.string().min(1).max(400).describe('Search query'),
  limit: z.number().min(1).max(25).optional().describe('Max results (default 10)'),
  dimensions: z.array(z.string()).max(5).optional().describe('Filter by dimensions')
};

const getNodesInputSchema = {
  nodeIds: z.array(z.number().int().positive()).min(1).max(10).describe('Node IDs to load')
};

const updateNodeInputSchema = {
  id: z.number().int().positive().describe('Node ID'),
  updates: z.object({
    title: z.string().optional().describe('New title'),
    content: z.string().optional().describe('Content to APPEND'),
    link: z.string().optional().describe('New link'),
    dimensions: z.array(z.string()).optional().describe('New dimensions (replaces existing)'),
    metadata: z.record(z.any()).optional().describe('New metadata')
  }).describe('Fields to update')
};

const createEdgeInputSchema = {
  sourceId: z.number().int().positive().describe("The 'subject' node (reads: source [explanation] target)"),
  targetId: z.number().int().positive().describe('Target node ID'),
  explanation: z.string().min(1).describe("Human-readable explanation. Should read as a sentence: 'Alice invented this technique'")
};

const updateEdgeInputSchema = {
  id: z.number().int().positive().describe('Edge ID'),
  explanation: z.string().min(1).describe('Updated explanation for this connection')
};

const queryEdgesInputSchema = {
  nodeId: z.number().int().positive().optional().describe('Find edges for this node'),
  limit: z.number().min(1).max(50).optional().describe('Max edges (default 25)')
};

const listDimensionsInputSchema = {};

const createDimensionInputSchema = {
  name: z.string().min(1).describe('Dimension name'),
  description: z.string().max(500).optional().describe('Description'),
  isPriority: z.boolean().optional().describe('Lock for auto-assignment')
};

const updateDimensionInputSchema = {
  name: z.string().min(1).describe('Current dimension name'),
  newName: z.string().optional().describe('New name (for renaming)'),
  description: z.string().max(500).optional().describe('New description'),
  isPriority: z.boolean().optional().describe('Lock/unlock dimension')
};

const deleteDimensionInputSchema = {
  name: z.string().min(1).describe('Dimension name to delete')
};

const readGuideInputSchema = {
  name: z.string().min(1).describe('Guide name (e.g. "edges", "creating-nodes", "schema")')
};

const writeGuideInputSchema = {
  name: z.string().min(1).describe('Guide name (lowercase, no spaces)'),
  content: z.string().min(1).describe('Full markdown content including YAML frontmatter (name, description)')
};

const deleteGuideInputSchema = {
  name: z.string().min(1).describe('Guide name to delete')
};

const searchContentInputSchema = {
  query: z.string().min(1).max(400).describe('Search text'),
  node_id: z.number().int().positive().optional().describe('Scope to a specific node\'s chunks'),
  limit: z.number().min(1).max(20).optional().describe('Max results (default 5)')
};

const sqliteQueryInputSchema = {
  sql: z.string().min(1).describe('The SQL query to execute. Must be a SELECT, WITH, or PRAGMA statement.'),
  format: z.enum(['json', 'table']).optional().describe('Output format (default json)')
};

// Helper to sanitize dimensions
function sanitizeDimensions(raw) {
  if (!Array.isArray(raw)) return [];
  const result = [];
  const seen = new Set();
  for (const value of raw) {
    if (typeof value !== 'string') continue;
    const trimmed = value.trim();
    if (!trimmed) continue;
    const lowered = trimmed.toLowerCase();
    if (seen.has(lowered)) continue;
    seen.add(lowered);
    result.push(trimmed);
    if (result.length >= 5) break;
  }
  return result;
}

// FTS5 helpers
function sanitizeFtsQuery(input) {
  return input
    .replace(/['"()*:^~{}[\]]/g, ' ')
    .trim()
    .split(/\s+/)
    .filter(w => w.length > 0 && !/^(AND|OR|NOT|NEAR)$/i.test(w))
    .join(' ');
}

let _ftsAvailability = null;

function checkFtsAvailability() {
  if (_ftsAvailability !== null) return _ftsAvailability;
  try {
    const db = getDb();
    const nodesFts = db.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='nodes_fts'").get();
    const chunksFts = db.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='chunks_fts'").get();
    _ftsAvailability = { nodes: !!nodesFts, chunks: !!chunksFts };
  } catch {
    _ftsAvailability = { nodes: false, chunks: false };
  }
  return _ftsAvailability;
}

function rebuildFtsIndexes() {
  const fts = checkFtsAvailability();
  if (!fts.nodes && !fts.chunks) return;

  const db = getDb();
  if (fts.nodes) {
    try {
      db.exec("INSERT INTO nodes_fts(nodes_fts) VALUES('rebuild')");
      log('Rebuilt nodes_fts index');
    } catch (err) {
      log('Warning: Failed to rebuild nodes_fts:', err.message);
      _ftsAvailability.nodes = false;
    }
  }
  if (fts.chunks) {
    try {
      db.exec("INSERT INTO chunks_fts(chunks_fts) VALUES('rebuild')");
      log('Rebuilt chunks_fts index');
    } catch (err) {
      log('Warning: Failed to rebuild chunks_fts:', err.message);
      _ftsAvailability.chunks = false;
    }
  }
}

// Security: Only allow read-only SQL statements
function isReadOnlyQuery(sql) {
  const normalized = sql.trim().toLowerCase();

  const allowedPrefixes = ['select', 'with', 'pragma'];
  const startsWithAllowed = allowedPrefixes.some(prefix =>
    normalized.startsWith(prefix)
  );

  if (!startsWithAllowed) return false;

  const dangerousPatterns = [
    /\binsert\b/i,
    /\bupdate\b/i,
    /\bdelete\b/i,
    /\bdrop\b/i,
    /\bcreate\b/i,
    /\balter\b/i,
    /\battach\b/i,
    /\bdetach\b/i,
    /\breindex\b/i,
    /\bvacuum\b/i,
    /\banalyze\b/i,
  ];

  return !dangerousPatterns.some(pattern => pattern.test(sql));
}

// Log to stderr (stdout is reserved for MCP protocol)
function log(...args) {
  console.error('[ra-h-standalone]', ...args);
}

async function main() {
  // Initialize database
  try {
    initDatabase();
    log('Database connected:', getDatabasePath());
    rebuildFtsIndexes();
  } catch (error) {
    log('ERROR:', error.message);
    process.exit(1);
  }

  const server = new McpServer(serverInfo, { instructions });

  // ========== CONTEXT TOOL ==========

  server.registerTool(
    'rah_get_context',
    {
      title: 'Get RA-H context',
      description: 'Get knowledge graph overview: stats, hub nodes (most connected), dimensions, recent activity, and available guides. Call this first to orient yourself. For deeper understanding, follow up with rah_read_guide("start-here").',
      inputSchema: {}
    },
    async () => {
      const context = nodeService.getContext();
      const guides = guideService.listGuides();
      context.guides = guides.map(g => ({ name: g.name, description: g.description, immutable: g.immutable }));

      // First-run welcome message
      if (context.stats.nodeCount === 0) {
        return {
          content: [{ type: 'text', text: 'Empty knowledge graph. This is a fresh start! Suggest adding the first node about something the user is working on or interested in.' }],
          structuredContent: {
            ...context,
            welcome: true,
            suggestion: 'Ask the user what they\'re working on or interested in, then create the first node.'
          }
        };
      }

      const summary = `Graph: ${context.stats.nodeCount} nodes, ${context.stats.edgeCount} edges, ${context.stats.dimensionCount} dimensions, ${guides.length} guides.`;
      return {
        content: [{ type: 'text', text: summary }],
        structuredContent: context
      };
    }
  );

  // ========== NODE TOOLS ==========

  server.registerTool(
    'rah_add_node',
    {
      title: 'Add RA-H node',
      description: 'Create a new node. Always search first (rah_search_nodes) to avoid duplicates. Title: max 160 chars, clear and descriptive. Use "link" ONLY for external content (URL, video, article) — omit for synthesis/ideas derived from existing nodes. "content" = your notes/analysis. "chunk" = verbatim source text. "description" = one-sentence summary for search. Assign 1-5 dimensions — call rah_list_dimensions first to use existing ones.',
      inputSchema: addNodeInputSchema
    },
    async ({ title, content, link, description, dimensions, metadata, chunk }) => {
      const normalizedDimensions = sanitizeDimensions(dimensions);
      if (normalizedDimensions.length === 0) {
        throw new Error('At least one dimension is required.');
      }

      const node = nodeService.createNode({
        title: title.trim(),
        content: content?.trim(),
        link: link?.trim(),
        description: description?.trim(),
        dimensions: normalizedDimensions,
        metadata: metadata || {},
        chunk: chunk?.trim()
      });

      const summary = `Created node #${node.id}: ${node.title} [${node.dimensions.join(', ')}]`;

      return {
        content: [{ type: 'text', text: summary }],
        structuredContent: {
          nodeId: node.id,
          title: node.title,
          dimensions: node.dimensions,
          message: summary
        }
      };
    }
  );

  server.registerTool(
    'rah_search_nodes',
    {
      title: 'Search RA-H nodes',
      description: 'Search nodes by keyword across title, description, and content fields. Multi-word queries find nodes containing all words (not exact phrases). Returns up to 25 results (default 10). Call before creating nodes to check for duplicates. Optionally filter by dimensions.',
      inputSchema: searchNodesInputSchema
    },
    async ({ query: searchQuery, limit = 10, dimensions }) => {
      const normalizedDimensions = sanitizeDimensions(dimensions || []);
      const safeLimit = Math.min(Math.max(limit, 1), 25);
      const trimmedQuery = searchQuery.trim();
      const fts = checkFtsAvailability();

      let nodes = null;

      // Try FTS5 first (handles multi-word queries naturally)
      if (fts.nodes) {
        const ftsQuery = sanitizeFtsQuery(trimmedQuery);
        if (ftsQuery) {
          try {
            let sql, params;

            if (normalizedDimensions.length > 0) {
              sql = `
                WITH fts_matches AS (
                  SELECT rowid, rank FROM nodes_fts WHERE nodes_fts MATCH ? LIMIT 100
                )
                SELECT n.id, n.title, n.description, n.content, n.link, n.updated_at,
                       COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                                 FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
                FROM fts_matches fm
                JOIN nodes n ON n.id = fm.rowid
                WHERE EXISTS (
                  SELECT 1 FROM node_dimensions nd
                  WHERE nd.node_id = n.id
                  AND nd.dimension IN (${normalizedDimensions.map(() => '?').join(',')})
                )
                ORDER BY fm.rank
                LIMIT ?
              `;
              params = [ftsQuery, ...normalizedDimensions, safeLimit];
            } else {
              sql = `
                WITH fts_matches AS (
                  SELECT rowid, rank FROM nodes_fts WHERE nodes_fts MATCH ? LIMIT ?
                )
                SELECT n.id, n.title, n.description, n.content, n.link, n.updated_at,
                       COALESCE((SELECT JSON_GROUP_ARRAY(d.dimension)
                                 FROM node_dimensions d WHERE d.node_id = n.id), '[]') as dimensions_json
                FROM fts_matches fm
                JOIN nodes n ON n.id = fm.rowid
                ORDER BY fm.rank
              `;
              params = [ftsQuery, safeLimit];
            }

            const rows = query(sql, params);
            nodes = rows.map(row => ({
              id: row.id,
              title: row.title,
              content: row.content ?? null,
              description: row.description ?? null,
              link: row.link ?? null,
              dimensions: JSON.parse(row.dimensions_json || '[]'),
              updated_at: row.updated_at
            }));
          } catch (err) {
            log('FTS search failed, falling back to LIKE:', err.message);
            nodes = null;
          }
        }
      }

      // Fallback: LIKE with word splitting (each word must appear somewhere)
      if (nodes === null) {
        const words = trimmedQuery.split(/\s+/).filter(w => w.length > 0);

        let sql = `
          SELECT n.id, n.title, n.description, n.content, n.link, 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 params = [];

        for (const word of words) {
          sql += ` AND (n.title LIKE ? COLLATE NOCASE OR n.description LIKE ? COLLATE NOCASE OR n.content LIKE ? COLLATE NOCASE)`;
          params.push(`%${word}%`, `%${word}%`, `%${word}%`);
        }

        if (normalizedDimensions.length > 0) {
          sql += ` AND EXISTS (
            SELECT 1 FROM node_dimensions nd
            WHERE nd.node_id = n.id
            AND nd.dimension IN (${normalizedDimensions.map(() => '?').join(',')})
          )`;
          params.push(...normalizedDimensions);
        }

        sql += ` ORDER BY n.updated_at DESC LIMIT ?`;
        params.push(safeLimit);

        const rows = query(sql, params);
        nodes = rows.map(row => ({
          id: row.id,
          title: row.title,
          content: row.content ?? null,
          description: row.description ?? null,
          link: row.link ?? null,
          dimensions: JSON.parse(row.dimensions_json || '[]'),
          updated_at: row.updated_at
        }));
      }

      const summary = nodes.length === 0
        ? 'No nodes found matching that query.'
        : `Found ${nodes.length} node(s).`;

      return {
        content: [{ type: 'text', text: summary }],
        structuredContent: {
          count: nodes.length,
          nodes
        }
      };
    }
  );

  server.registerTool(
    'rah_get_nodes',
    {
      title: 'Get RA-H nodes by ID',
      description: 'Load full node records by their IDs (max 10 per call). Chunks over 10K chars are truncated — check chunk_truncated and chunk_length fields. For full text, use rah_search_content to search or rah_sqlite_query with substr() to read sections.',
      inputSchema: getNodesInputSchema
    },
    async ({ nodeIds }) => {
      const uniqueIds = [...new Set(nodeIds.filter(id => Number.isFinite(id) && id > 0))];
      if (uniqueIds.length === 0) {
        throw new Error('No valid node IDs provided.');
      }

      const CHUNK_LIMIT = 10000;
      const nodes = [];
      for (const id of uniqueIds) {
        const node = nodeService.getNodeById(id);
        if (node) {
          const rawChunk = node.chunk ?? null;
          const chunkTruncated = rawChunk ? rawChunk.length > CHUNK_LIMIT : false;

          nodes.push({
            id: node.id,
            title: node.title,
            content: node.content ?? null,
            description: node.description ?? null,
            link: node.link ?? null,
            chunk: chunkTruncated ? rawChunk.substring(0, CHUNK_LIMIT) : rawChunk,
            chunk_truncated: chunkTruncated,
            chunk_length: rawChunk ? rawChunk.length : 0,
            dimensions: node.dimensions || [],
            metadata: node.metadata ?? null,
            updated_at: node.updated_at
          });
        }
      }

      return {
        content: [{ type: 'text', text: `Loaded ${nodes.length} of ${uniqueIds.length} nodes.` }],
        structuredContent: {
          count: nodes.length,
          nodes
        }
      };
    }
  );

  server.registerTool(
    'rah_update_node',
    {
      title: 'Update RA-H node',
      description: 'Update an existing node. Content is APPENDED to existing content (not replaced). Dimensions are REPLACED entirely with the new array. Title, description, and link are overwritten.',
      inputSchema: updateNodeInputSchema
    },
    async ({ id, updates }) => {
      if (!updates || Object.keys(updates).length === 0) {
        throw new Error('At least one field must be provided in updates.');
      }

      const node = nodeService.updateNode(id, updates, { appendContent: true });

      return {
        content: [{ type: 'text', text: `Updated node #${id}` }],
        structuredContent: {
          success: true,
          nodeId: node.id,
          message: `Updated node #${id}`
        }
      };
    }
  );

  // ========== EDGE TOOLS ==========

  server.registerTool(
    'rah_create_edge',
    {
      title: 'Create RA-H edge',
      description: 'Connect two nodes with an edge. Edges are the most valuable part of the graph — they represent understanding, not proximity. Direction matters: reads as sourceId → [explanation] → targetId. The explanation should read as a sentence (e.g. "invented this technique", "contradicts the claim in").',
      inputSchema: createEdgeInputSchema
    },
    async ({ sourceId, targetId, explanation }) => {
      const edge = edgeService.createEdge({
        from_node_id: sourceId,
        to_node_id: targetId,
        explanation: explanation.trim(),
        source: 'mcp'
      });

      return {
        content: [{ type: 'text', text: `Created edge from #${sourceId} to #${targetId}` }],
        structuredContent: {
          success: true,
          edgeId: edge.id,
          message: `Created edge from #${sourceId} to #${targetId}`
        }
      };
    }
  );

  server.registerTool(
    'rah_update_edge',
    {
      title: 'Update RA-H edge',
      description: 'Update an edge explanation. Use when a connection needs a better or corrected explanation.',
      inputSchema: updateEdgeInputSchema
    },
    async ({ id, explanation }) => {
      const edge = edgeService.updateEdge(id, { explanation: explanation.trim() });

      return {
        content: [{ type: 'text', text: `Updated edge #${id}` }],
        structuredContent: {
          success: true,
          edgeId: edge.id,
          message: `Updated edge #${id}`
        }
      };
    }
  );

  server.registerTool(
    'rah_query_edges',
    {
      title: 'Query RA-H edges',
      description: 'Find edges/connections. Optionally filter by nodeId to see all connections for a specific node. Returns up to 50 edges (default 25) with edge IDs, connected node IDs, and explanations.',
      inputSchema: queryEdgesInputSchema
    },
    async ({ nodeId, limit = 25 }) => {
      const edges = edgeService.getEdges({
        nodeId,
        limit: Math.min(Math.max(limit, 1), 50)
      });

      return {
        content: [{ type: 'text', text: `Found ${edges.length} edge(s).` }],
        structuredContent: {
          count: edges.length,
          edges: edges.map(e => ({
            id: e.id,
            from_node_id: e.from_node_id,
            to_node_id: e.to_node_id,
            type: e.context?.type ?? null,
            explanation: e.context?.explanation ?? null
          }))
        }
      };
    }
  );

  // ========== DIMENSION TOOLS ==========

  server.registerTool(
    'rah_list_dimensions',
    {
      title: 'List RA-H dimensions',
      description: 'Get all dimensions with node counts.',
      inputSchema: listDimensionsInputSchema
    },
    async () => {
      const dimensions = dimensionService.getDimensions();

      return {
        content: [{ type: 'text', text: `Found ${dimensions.length} dimension(s).` }],
        structuredContent: {
          count: dimensions.length,
          dimensions
        }
      };
    }
  );

  server.registerTool(
    'rah_create_dimension',
    {
      title: 'Create RA-H dimension',
      description: 'Create a new dimension/category. Use lowercase, singular form (e.g. "biology" not "Biology" or "biologies"). Set isPriority=true to lock it for automatic assignment to new nodes. Always include a description.',
      inputSchema: createDimensionInputSchema
    },
    async ({ name, description, isPriority }) => {
      const dimension = dimensionService.createDimension({
        name,
        description,
        isPriority
      });

      return {
        content: [{ type: 'text', text: `Created dimension: ${dimension.dimension}` }],
        structuredContent: {
          success: true,
          dimension: dimension.dimension,
          message: `Created dimension: ${dimension.dimension}`
        }
      };
    }
  );

  server.registerTool(
    'rah_update_dimension',
    {
      title: 'Update RA-H dimension',
      description: 'Update or rename a dimension.',
      inputSchema: updateDimensionInputSchema
    },
    async ({ name, newName, description, isPriority }) => {
      const result = dimensionService.updateDimension({
        name,
        currentName: name,
        newName,
        description,
        isPriority
      });

      return {
        content: [{ type: 'text', text: `Updated dimension: ${result.dimension}` }],
        structuredContent: {
          success: true,
          dimension: result.dimension,
          message: `Updated dimension: ${result.dimension}`
        }
      };
    }
  );

  server.registerTool(
    'rah_delete_dimension',
    {
      title: 'Delete RA-H dimension',
      description: 'Delete a dimension and remove it from all nodes.',
      inputSchema: deleteDimensionInputSchema
    },
    async ({ name }) => {
      const result = dimensionService.deleteDimension(name);

      return {
        content: [{ type: 'text', text: `Deleted dimension: ${name}` }],
        structuredContent: {
          success: true,
          message: `Deleted dimension: ${name}`
        }
      };
    }
  );

  // ========== GUIDE TOOLS ==========

  server.registerTool(
    'rah_list_guides',
    {
      title: 'List RA-H guides',
      description: 'List all guides — system guides (immutable reference docs) and user-created guides (custom workflows and preferences). Read "start-here" first for orientation.',
      inputSchema: {}
    },
    async () => {
      const guides = guideService.listGuides();

      return {
        content: [{ type: 'text', text: `Found ${guides.length} guide(s).` }],
        structuredContent: {
          count: guides.length,
          guides
        }
      };
    }
  );

  server.registerTool(
    'rah_read_guide',
    {
      title: 'Read RA-H guide',
      description: 'Read a guide by name. Returns full markdown with procedural instructions. Read "start-here" for master orientation. Call rah_list_guides to see all available guides.',
      inputSchema: readGuideInputSchema
    },
    async ({ name }) => {
      const guide = guideService.readGuide(name);

      if (!guide) {
        throw new Error(`Guide "${name}" not found. Call rah_list_guides to see available guides.`);
      }

      return {
        content: [{ type: 'text', text: guide.content }],
        structuredContent: guide
      };
    }
  );

  server.registerTool(
    'rah_write_guide',
    {
      title: 'Write RA-H guide',
      description: 'Create or update a custom guide. System guides cannot be modified. Content should be markdown with YAML frontmatter (name, description).',
      inputSchema: writeGuideInputSchema
    },
    async ({ name, content }) => {
      const result = guideService.writeGuide(name, content);

      if (!result.success) {
        throw new Error(result.error);
      }

      return {
        content: [{ type: 'text', text: `Guide "${name}" saved.` }],
        structuredContent: {
          success: true,
          name,
          message: `Guide "${name}" saved.`
        }
      };
    }
  );

  server.registerTool(
    'rah_delete_guide',
    {
      title: 'Delete RA-H guide',
      description: 'Delete a custom guide. System guides cannot be deleted.',
      inputSchema: deleteGuideInputSchema
    },
    async ({ name }) => {
      const result = guideService.deleteGuide(name);

      if (!result.success) {
        throw new Error(result.error);
      }

      return {
        content: [{ type: 'text', text: `Guide "${name}" deleted.` }],
        structuredContent: {
          success: true,
          name,
          message: `Guide "${name}" deleted.`
        }
      };
    }
  );

  // ========== CONTENT SEARCH TOOL ==========

  server.registerTool(
    'rah_search_content',
    {
      title: 'Search RA-H source content',
      description: 'Search through source content (transcripts, books, articles) stored as chunks. Use when you need to find specific text within a node\'s full source material. For node-level search (titles, descriptions), use rah_search_nodes instead.',
      inputSchema: searchContentInputSchema
    },
    async ({ query: searchQuery, node_id, limit = 5 }) => {
      const db = getDb();

      // Check if chunks table exists
      const tableCheck = db.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='chunks'").get();
      if (!tableCheck) {
        return {
          content: [{ type: 'text', text: 'No chunks table found. Source content has not been chunked yet. Use rah_get_nodes to read the raw chunk field instead.' }],
          structuredContent: { count: 0, chunks: [], note: 'chunks table does not exist' }
        };
      }

      const safeLimit = Math.min(Math.max(limit, 1), 20);
      const trimmedQuery = searchQuery.trim();
      const fts = checkFtsAvailability();

      let results = null;

      // Try FTS5 first (handles multi-word, relevance ranked)
      if (fts.chunks) {
        const ftsQuery = sanitizeFtsQuery(trimmedQuery);
        if (ftsQuery) {
          try {
            let sql, params;

            if (node_id) {
              sql = `
                SELECT c.id, c.node_id, c.chunk_idx, c.text, n.title as node_title
                FROM chunks c
                JOIN nodes n ON c.node_id = n.id
                WHERE c.node_id = ?
                AND c.id IN (SELECT rowid FROM chunks_fts WHERE chunks_fts MATCH ?)
                ORDER BY c.chunk_idx ASC
                LIMIT ?
              `;
              params = [node_id, ftsQuery, safeLimit];
            } else {
              sql = `
                WITH fts_matches AS (
                  SELECT rowid, rank FROM chunks_fts WHERE chunks_fts MATCH ? LIMIT ?
                )
                SELECT c.id, c.node_id, c.chunk_idx, c.text, n.title as node_title
                FROM fts_matches fm
                JOIN chunks c ON c.id = fm.rowid
                JOIN nodes n ON c.node_id = n.id
                ORDER BY fm.rank
              `;
              params = [ftsQuery, safeLimit];
            }

            results = query(sql, params);
          } catch (err) {
            log('FTS content search failed, falling back to LIKE:', err.message);
            results = null;
          }
        }
      }

      // Fallback: LIKE with word splitting
      if (results === null) {
        const words = trimmedQuery.split(/\s+/).filter(w => w.length > 0);

        let sql = `
          SELECT c.id, c.node_id, c.chunk_idx, c.text, n.title as node_title
          FROM chunks c
          JOIN nodes n ON c.node_id = n.id
          WHERE 1=1
        `;
        const params = [];

        if (node_id) {
          sql += ` AND c.node_id = ?`;
          params.push(node_id);
        }

        for (const word of words) {
          sql += ` AND c.text LIKE ? COLLATE NOCASE`;
          params.push(`%${word}%`);
        }

        sql += ` ORDER BY n.updated_at DESC, c.chunk_idx ASC LIMIT ?`;
        params.push(safeLimit);

        results = query(sql, params);
      }

      const summary = results.length === 0
        ? 'No matching content found in chunks.'
        : `Found ${results.length} chunk(s) matching "${trimmedQuery}".`;

      return {
        content: [{ type: 'text', text: summary }],
        structuredContent: {
          count: results.length,
          chunks: results.map(r => ({
            id: r.id,
            node_id: r.node_id,
            chunk_idx: r.chunk_idx,
            text: r.text,
            node_title: r.node_title
          }))
        }
      };
    }
  );

  // ========== SQL QUERY TOOL ==========

  server.registerTool(
    'rah_sqlite_query',
    {
      title: 'Execute read-only SQL',
      description: 'Execute read-only SQL queries against the knowledge graph database. Tables: nodes, edges, dimensions, node_dimensions, chunks. Use PRAGMA table_info(tablename) for schema. Only SELECT/WITH/PRAGMA allowed.',
      inputSchema: sqliteQueryInputSchema
    },
    async ({ sql: userSql, format = 'json' }) => {
      if (!isReadOnlyQuery(userSql)) {
        throw new Error('Only SELECT, WITH, and PRAGMA statements are allowed. Write operations must use dedicated tools.');
      }

      try {
        const rows = query(userSql);
        const rowCount = Array.isArray(rows) ? rows.length : 0;

        if (format === 'table' && Array.isArray(rows) && rows.length > 0) {
          // Simple table format
          const cols = Object.keys(rows[0]);
          const header = cols.join(' | ');
          const separator = cols.map(c => '-'.repeat(c.length)).join(' | ');
          const body = rows.map(r => cols.map(c => String(r[c] ?? '')).join(' | ')).join('\n');
          const tableStr = `${header}\n${separator}\n${body}`;

          return {
            content: [{ type: 'text', text: `${rowCount} row(s).\n\n${tableStr}` }],
            structuredContent: { count: rowCount, rows }
          };
        }

        return {
          content: [{ type: 'text', text: `${rowCount} row(s).` }],
          structuredContent: { count: rowCount, rows: Array.isArray(rows) ? rows : [rows] }
        };
      } catch (err) {
        throw new Error(`SQL error: ${err.message}`);
      }
    }
  );

  // Connect transport
  const transport = new StdioServerTransport();
  await server.connect(transport);
  log('MCP server ready');

  // Handle graceful shutdown
  process.on('SIGINT', () => {
    log('Shutting down...');
    closeDatabase();
    process.exit(0);
  });

  process.on('SIGTERM', () => {
    log('Shutting down...');
    closeDatabase();
    process.exit(0);
  });
}

main().catch((error) => {
  console.error('[ra-h-standalone] Fatal error:', error);
  process.exit(1);
});