Add auto-capture system (Milestone 2)

- Add capture configuration system with modes: always, manual, decisions, off - Add Ollama-based conversation summarization and extraction - Add deduplication via embedding similarity (merge >0.90, link 0.75-0.90) - Add CLI commands: capture, capture-hook, config - Add MCP tools: memory_capture, memory_remember, memory_capture_config - Include summary.ts (previously uncommitted)
2026-02-03 09:59:49 +01:00
12 changed files with 775 additions and 648 deletions
--- a/src/cli/commands/capture.ts
+++ b/src/cli/commands/capture.ts
@@ -0,0 +1,176 @@
 import { Command } from 'commander';
 import chalk from 'chalk';
 import { captureConversation, captureText, getCaptureConfig, setCaptureConfig, CaptureMode } from '../../core/capture';
 const VALID_MODES: CaptureMode[] = ['always', 'manual', 'decisions', 'off'];
 export const captureCommand = new Command('capture')
  .description('Capture text or conversation as a memory node')
  .argument('[text]', 'Text to capture (or pipe via stdin)')
  .option('--tags <tags>', 'Comma-separated tags')
  .option('--source <source>', 'Source identifier', 'manual')
  .action(async (text: string | undefined, opts) => {
    let content = text;
    // Read from stdin if no text provided
    if (!content) {
      content = await readStdin();
    }
    if (!content || content.trim().length === 0) {
      console.error(chalk.red('No text provided. Pass text as argument or pipe via stdin.'));
      process.exit(1);
    }
    const tags = opts.tags ? opts.tags.split(',').map((t: string) => t.trim()) : [];
    const result = await captureText(content, { tags, source: opts.source });
    if (!result.captured) {
      console.log(chalk.yellow(`⚠ Not captured: ${result.reason}`));
      return;
    }
    console.log(chalk.green(`✓ Memory ${result.action}`));
    if (result.node) {
      console.log(`  ID:    ${chalk.cyan(result.node.id)}`);
      console.log(`  Title: ${result.node.title}`);
      if (result.node.tags.length) console.log(`  Tags:  ${result.node.tags.join(', ')}`);
    }
    if (result.reason) {
      console.log(`  ${chalk.dim(result.reason)}`);
    }
  });
 export const captureHookCommand = new Command('capture-hook')
  .description('Hook handler for Claude Code auto-capture (receives JSON on stdin)')
  .option('--session <id>', 'Session ID')
  .action(async (opts) => {
    const input = await readStdin();
    if (!input) {
      // Silent exit - hook may be called with empty input
      process.exit(0);
    }
    let data: { conversation?: string; files_changed?: string[]; session_id?: string };
    try {
      data = JSON.parse(input);
    } catch {
      // Not JSON, treat as plain conversation text
      data = { conversation: input };
    }
    const conversation = data.conversation;
    if (!conversation) {
      process.exit(0);
    }
    const result = await captureConversation({
      conversation,
      sessionId: data.session_id || opts.session,
      filesChanged: data.files_changed,
      source: 'claude-code',
    });
    // Output result as JSON for hook system
    console.log(JSON.stringify({
      captured: result.captured,
      action: result.action,
      nodeId: result.node?.id,
      reason: result.reason,
    }));
  });
 export const configCommand = new Command('config')
  .description('Manage capture configuration')
  .argument('<action>', 'Action: get, set, or list')
  .argument('[key]', 'Config key (for get/set)')
  .argument('[value]', 'Config value (for set)')
  .action(async (action: string, key?: string, value?: string) => {
    const config = getCaptureConfig();
    if (action === 'list') {
      console.log(chalk.bold('Capture Configuration:'));
      console.log(`  mode:              ${chalk.cyan(config.mode)}`);
      console.log(`  minLength:         ${config.minLength}`);
      console.log(`  excludePatterns:   ${config.excludePatterns.length ? config.excludePatterns.join(', ') : chalk.dim('(none)')}`);
      console.log(`  autoTag:           ${config.autoTag}`);
      console.log(`  linkRelated:       ${config.linkRelated}`);
      console.log(`  similarityThreshold: ${config.similarityThreshold}`);
      console.log(`  mergeThreshold:    ${config.mergeThreshold}`);
      return;
    }
    if (action === 'get') {
      if (!key) {
        console.error(chalk.red('Key required for get'));
        process.exit(1);
      }
      if (!(key in config)) {
        console.error(chalk.red(`Unknown config key: ${key}`));
        process.exit(1);
      }
      const val = config[key as keyof typeof config];
      console.log(Array.isArray(val) ? val.join(', ') : String(val));
      return;
    }
    if (action === 'set') {
      if (!key || value === undefined) {
        console.error(chalk.red('Key and value required for set'));
        process.exit(1);
      }
      let parsedValue: any = value;
      // Parse value based on key type
      if (key === 'mode') {
        if (!VALID_MODES.includes(value as CaptureMode)) {
          console.error(chalk.red(`Invalid mode. Must be one of: ${VALID_MODES.join(', ')}`));
          process.exit(1);
        }
        parsedValue = value;
      } else if (key === 'minLength' || key === 'similarityThreshold' || key === 'mergeThreshold') {
        parsedValue = parseFloat(value);
        if (isNaN(parsedValue)) {
          console.error(chalk.red('Value must be a number'));
          process.exit(1);
        }
      } else if (key === 'autoTag' || key === 'linkRelated') {
        parsedValue = value === 'true' || value === '1';
      } else if (key === 'excludePatterns') {
        parsedValue = value.split(',').map(s => s.trim()).filter(Boolean);
      } else {
        console.error(chalk.red(`Unknown config key: ${key}`));
        process.exit(1);
      }
      setCaptureConfig({ [key]: parsedValue });
      console.log(chalk.green(`✓ Set ${key} = ${JSON.stringify(parsedValue)}`));
      return;
    }
    console.error(chalk.red('Invalid action. Use: get, set, or list'));
    process.exit(1);
  });
 async function readStdin(): Promise<string> {
  return new Promise((resolve) => {
    // Check if stdin has data (non-TTY mode)
    if (process.stdin.isTTY) {
      resolve('');
      return;
    }
    let data = '';
    process.stdin.setEncoding('utf8');
    process.stdin.on('data', (chunk) => { data += chunk; });
    process.stdin.on('end', () => { resolve(data.trim()); });
    // Timeout after 100ms if no data
    setTimeout(() => {
      if (!data) resolve('');
    }, 100);
  });
 }
--- a/src/cli/commands/config.ts
+++ b/src/cli/commands/config.ts
@@ -1,81 +0,0 @@
 import { Command } from 'commander';
 import chalk from 'chalk';
 import { getConfig, setConfig, listConfig, resetConfig, CortexConfig } from '../../core/config';
 export const configCommand = new Command('config')
  .description('Manage Cortex configuration');
 configCommand
  .command('get <key>')
  .description('Get a config value')
  .action((key: string) => {
    try {
      const value = getConfig(key as keyof CortexConfig);
      console.log(value);
    } catch (err) {
      console.error(chalk.red(`Unknown config key: ${key}`));
      process.exit(1);
    }
  });
 configCommand
  .command('set <key> <value>')
  .description('Set a config value')
  .action((key: string, value: string) => {
    // Validate key exists
    const validKeys = [
      'context.maxTokens',
      'context.maxNodes',
      'context.includeRecent',
      'context.includeProject',
      'context.includeTasks',
      'context.includeDecisions',
    ];
    if (!validKeys.includes(key)) {
      console.error(chalk.red(`Unknown config key: ${key}`));
      console.error(chalk.dim(`Valid keys: ${validKeys.join(', ')}`));
      process.exit(1);
    }
    // Parse value based on key type
    let parsed: string | number | boolean = value;
    if (key.startsWith('context.max')) {
      parsed = parseInt(value, 10);
      if (isNaN(parsed)) {
        console.error(chalk.red(`Invalid number: ${value}`));
        process.exit(1);
      }
    } else if (key.startsWith('context.include')) {
      if (value !== 'true' && value !== 'false') {
        console.error(chalk.red(`Invalid boolean: ${value} (use true or false)`));
        process.exit(1);
      }
      parsed = value === 'true';
    }
    setConfig(key as keyof CortexConfig, parsed as any);
    console.log(chalk.green(`Set ${key} = ${parsed}`));
  });
 configCommand
  .command('list')
  .description('List all config values')
  .action(() => {
    const configs = listConfig();
    console.log(chalk.bold('Configuration:'));
    console.log();
    for (const { key, value, isDefault } of configs) {
      const displayValue = isDefault ? chalk.dim(`${value} (default)`) : chalk.cyan(value);
      console.log(`  ${chalk.yellow(key)}: ${displayValue}`);
    }
  });
 configCommand
  .command('reset <key>')
  .description('Reset a config key to default')
  .action((key: string) => {
    resetConfig(key as keyof CortexConfig);
    console.log(chalk.green(`Reset ${key} to default`));
  });
--- a/src/cli/commands/context.ts
+++ b/src/cli/commands/context.ts
@@ -1,85 +0,0 @@
 import { Command } from 'commander';
 import chalk from 'chalk';
 import * as path from 'path';
 import { gatherContext, DEFAULT_CONTEXT_CONFIG } from '../../core/context';
 export const contextCommand = new Command('context')
  .description('Preview or inject context for a Claude session')
  .option('-p, --project <name>', 'Project name (defaults to current directory name)')
  .option('-q, --query <text>', 'Additional semantic search query')
  .option('--max-tokens <n>', 'Maximum tokens', String(DEFAULT_CONTEXT_CONFIG.maxTokens))
  .option('--max-nodes <n>', 'Maximum nodes', String(DEFAULT_CONTEXT_CONFIG.maxNodes))
  .option('--format <fmt>', 'Output format: markdown or json', 'markdown')
  .option('--no-recent', 'Exclude recent activity')
  .option('--no-tasks', 'Exclude open tasks')
  .option('--no-decisions', 'Exclude decisions')
  .action(async (opts) => {
    const project = opts.project ?? path.basename(process.cwd());
    const result = await gatherContext({
      project,
      semanticQuery: opts.query,
      config: {
        maxTokens: parseInt(opts.maxTokens),
        maxNodes: parseInt(opts.maxNodes),
        includeRecent: opts.recent !== false,
        includeTasks: opts.tasks !== false,
        includeDecisions: opts.decisions !== false,
      },
    });
    if (opts.format === 'json') {
      console.log(JSON.stringify({
        project,
        nodeCount: result.nodes.length,
        nodes: result.nodes.map(r => ({
          id: r.node.id,
          kind: r.node.kind,
          title: r.node.title,
          score: r.score,
          reason: r.reason,
        })),
      }, null, 2));
      return;
    }
    // Markdown output
    if (result.nodes.length === 0) {
      console.log(chalk.yellow('No relevant context found.'));
      return;
    }
    console.log(chalk.cyan(`# Context for ${project}`));
    console.log(chalk.dim(`(${result.nodes.length} nodes)`));
    console.log();
    console.log(result.formatted);
  });
 /**
 * Hook command for Claude Code integration
 * Outputs context to stdout for injection
 */
 export const contextHookCommand = new Command('context-hook')
  .description('Hook handler for Claude Code session start (outputs context to stdout)')
  .option('-p, --project <name>', 'Project name (defaults to current directory name)')
  .option('--max-tokens <n>', 'Maximum tokens', String(DEFAULT_CONTEXT_CONFIG.maxTokens))
  .action(async (opts) => {
    const project = opts.project ?? path.basename(process.cwd());
    const result = await gatherContext({
      project,
      config: {
        maxTokens: parseInt(opts.maxTokens),
      },
    });
    if (result.nodes.length === 0) {
      // Output nothing if no context
      return;
    }
    // Output markdown directly to stdout for Claude to consume
    console.log(`<cortex-context project="${project}">`);
    console.log(result.formatted);
    console.log('</cortex-context>');
  });
--- a/src/cli/index.ts
+++ b/src/cli/index.ts
@@ -11,8 +11,7 @@ import { graphCommand } from './commands/graph';
 import { serveCommand } from './commands/serve';
 import { decayCommand } from './commands/decay';
 import { childrenCommand } from './commands/children';
-import { contextCommand, contextHookCommand } from './commands/context';
+import { captureCommand, captureHookCommand, configCommand } from './commands/capture';
 import { configCommand } from './commands/config';
 import { closeDb } from '../core/db';
 const program = new Command();
@@ -33,8 +32,8 @@ program.addCommand(graphCommand);
 program.addCommand(serveCommand);
 program.addCommand(decayCommand);
 program.addCommand(childrenCommand);
-program.addCommand(contextCommand);
+program.addCommand(captureCommand);
-program.addCommand(contextHookCommand);
+program.addCommand(captureHookCommand);
 program.addCommand(configCommand);
 program.hook('postAction', () => {
--- a/src/core/capture/config.ts
+++ b/src/core/capture/config.ts
@@ -0,0 +1,68 @@
 import { getDb } from '../db';
 export type CaptureMode = 'always' | 'manual' | 'decisions' | 'off';
 export interface CaptureConfig {
  mode: CaptureMode;
  minLength: number;
  excludePatterns: string[];
  autoTag: boolean;
  linkRelated: boolean;
  similarityThreshold: number;
  mergeThreshold: number;
 }
 const DEFAULT_CONFIG: CaptureConfig = {
  mode: 'always',
  minLength: 100,
  excludePatterns: [],
  autoTag: true,
  linkRelated: true,
  similarityThreshold: 0.75,
  mergeThreshold: 0.90,
 };
 function ensureConfigTable(): void {
  const db = getDb();
  db.exec(`
    CREATE TABLE IF NOT EXISTS system_config (
      key TEXT PRIMARY KEY,
      value TEXT NOT NULL,
      updated_at INTEGER NOT NULL
    )
  `);
 }
 export function getCaptureConfig(): CaptureConfig {
  ensureConfigTable();
  const db = getDb();
  const row = db.prepare('SELECT value FROM system_config WHERE key = ?').get('capture') as { value: string } | undefined;
  if (!row) return DEFAULT_CONFIG;
  try {
    return { ...DEFAULT_CONFIG, ...JSON.parse(row.value) };
  } catch {
    return DEFAULT_CONFIG;
  }
 }
 export function setCaptureConfig(updates: Partial<CaptureConfig>): CaptureConfig {
  ensureConfigTable();
  const db = getDb();
  const current = getCaptureConfig();
  const updated = { ...current, ...updates };
  db.prepare(`
    INSERT INTO system_config (key, value, updated_at) VALUES (?, ?, ?)
    ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = excluded.updated_at
  `).run('capture', JSON.stringify(updated), Date.now());
  return updated;
 }
 export function getConfigValue<K extends keyof CaptureConfig>(key: K): CaptureConfig[K] {
  return getCaptureConfig()[key];
 }
 export function setConfigValue<K extends keyof CaptureConfig>(key: K, value: CaptureConfig[K]): void {
  setCaptureConfig({ [key]: value } as Partial<CaptureConfig>);
 }
--- a/src/core/capture/dedupe.ts
+++ b/src/core/capture/dedupe.ts
@@ -0,0 +1,113 @@
 import { listNodes, addEdge, updateNode } from '../store';
 import { getEmbedding } from '../search/ollama';
 import { cosineSimilarity } from '../search/vector';
 import { Node } from '../../types';
 import { getCaptureConfig } from './config';
 export interface SimilarNode {
  node: Node;
  similarity: number;
 }
 export interface DedupeResult {
  action: 'create' | 'merge' | 'link';
  existingNode?: Node;
  similarity?: number;
 }
 export async function findSimilarNodes(
  text: string,
  limit: number = 5
 ): Promise<SimilarNode[]> {
  const embedding = await getEmbedding(text);
  if (!embedding) return [];
  const nodes = listNodes({ includeStale: false });
  const withEmbeddings = nodes.filter(n => n.embedding && n.embedding.length > 0);
  const scored: SimilarNode[] = [];
  for (const node of withEmbeddings) {
    const similarity = cosineSimilarity(embedding, node.embedding!);
    if (similarity > 0.5) {
      scored.push({ node, similarity });
    }
  }
  return scored
    .sort((a, b) => b.similarity - a.similarity)
    .slice(0, limit);
 }
 export async function checkDuplicate(
  summary: string,
  content: string
 ): Promise<DedupeResult> {
  const config = getCaptureConfig();
  const textToCompare = `${summary} ${content}`;
  const similar = await findSimilarNodes(textToCompare, 1);
  if (similar.length === 0) {
    return { action: 'create' };
  }
  const { node, similarity } = similar[0];
  if (similarity >= config.mergeThreshold) {
    return {
      action: 'merge',
      existingNode: node,
      similarity,
    };
  }
  if (similarity >= config.similarityThreshold) {
    return {
      action: 'link',
      existingNode: node,
      similarity,
    };
  }
  return { action: 'create' };
 }
 export async function mergeIntoNode(
  existingId: string,
  newSummary: string,
  newContent: string,
  newTags: string[]
 ): Promise<Node | null> {
  const existing = listNodes({ includeStale: false }).find(n => n.id === existingId);
  if (!existing) return null;
  // Append new content with timestamp
  const timestamp = new Date().toISOString().slice(0, 10);
  const mergedContent = existing.content
    ? `${existing.content}\n\n---\n[${timestamp}]\n${newContent}`
    : newContent;
  // Merge tags (dedupe)
  const mergedTags = [...new Set([...existing.tags, ...newTags])];
  // Update the existing node
  return updateNode(existingId, {
    content: mergedContent,
    tags: mergedTags,
    metadata: {
      ...existing.metadata,
      lastMergedAt: Date.now(),
      mergeCount: (existing.metadata.mergeCount || 0) + 1,
    },
  });
 }
 export async function linkRelatedNode(
  newNodeId: string,
  existingNodeId: string
 ): Promise<void> {
  addEdge(newNodeId, existingNodeId, 'relates_to', {
    reason: 'auto-capture-similarity',
    linkedAt: Date.now(),
  });
 }
--- a/src/core/capture/index.ts
+++ b/src/core/capture/index.ts
@@ -0,0 +1,192 @@
 import { addNode } from '../store';
 import { getCaptureConfig, CaptureConfig } from './config';
 import { extractMemoryData, shouldCapture, ExtractedMemory } from './summarize';
 import { checkDuplicate, mergeIntoNode, linkRelatedNode } from './dedupe';
 import { Node } from '../../types';
 export { getCaptureConfig, setCaptureConfig, CaptureMode, CaptureConfig } from './config';
 export { extractMemoryData, shouldCapture, ExtractedMemory } from './summarize';
 export { findSimilarNodes, checkDuplicate, mergeIntoNode } from './dedupe';
 export interface CaptureInput {
  conversation: string;
  sessionId?: string;
  filesChanged?: string[];
  source?: string;
 }
 export interface CaptureResult {
  captured: boolean;
  action: 'created' | 'merged' | 'linked' | 'skipped';
  node?: Node;
  reason?: string;
 }
 export async function captureConversation(input: CaptureInput): Promise<CaptureResult> {
  const config = getCaptureConfig();
  // Check if capture is enabled
  if (config.mode === 'off') {
    return { captured: false, action: 'skipped', reason: 'capture disabled' };
  }
  // Check minimum length
  if (!shouldCapture(input.conversation, config.minLength)) {
    return { captured: false, action: 'skipped', reason: 'conversation too short or trivial' };
  }
  // Check exclude patterns
  for (const pattern of config.excludePatterns) {
    try {
      if (new RegExp(pattern, 'i').test(input.conversation)) {
        return { captured: false, action: 'skipped', reason: `matched exclude pattern: ${pattern}` };
      }
    } catch {
      // Invalid regex, skip
    }
  }
  // Extract memory data using Ollama
  const extracted = await extractMemoryData(input.conversation);
  if (!extracted) {
    return { captured: false, action: 'skipped', reason: 'failed to extract memory data' };
  }
  // For "decisions" mode, only capture if decisions were found
  if (config.mode === 'decisions' && extracted.decisions.length === 0) {
    return { captured: false, action: 'skipped', reason: 'no decisions found (decisions mode)' };
  }
  // Build content
  const contentParts: string[] = [extracted.summary];
  if (extracted.decisions.length > 0) {
    contentParts.push('\n## Decisions');
    for (const d of extracted.decisions) {
      contentParts.push(`- ${d}`);
    }
  }
  if (extracted.filesDiscussed.length > 0 || input.filesChanged?.length) {
    const files = [...new Set([...extracted.filesDiscussed, ...(input.filesChanged || [])])];
    contentParts.push('\n## Files');
    for (const f of files) {
      contentParts.push(`- ${f}`);
    }
  }
  const content = contentParts.join('\n');
  // Check for duplicates
  const dedupeResult = await checkDuplicate(extracted.summary, content);
  // Build tags
  const tags = ['auto-capture'];
  if (config.autoTag && extracted.topics.length > 0) {
    tags.push(...extracted.topics);
  }
  if (input.source) {
    tags.push(`source:${input.source}`);
  }
  if (dedupeResult.action === 'merge' && dedupeResult.existingNode) {
    // Merge into existing node
    const merged = await mergeIntoNode(
      dedupeResult.existingNode.id,
      extracted.summary,
      content,
      tags
    );
    return {
      captured: true,
      action: 'merged',
      node: merged || undefined,
      reason: `merged with existing node (similarity: ${(dedupeResult.similarity! * 100).toFixed(1)}%)`,
    };
  }
  // Create new node
  const node = await addNode({
    kind: 'memory',
    title: extracted.summary.slice(0, 100),
    content,
    tags,
    status: 'active',
    metadata: {
      sessionId: input.sessionId,
      filesChanged: input.filesChanged,
      source: input.source || 'claude-code',
      capturedAt: Date.now(),
      decisions: extracted.decisions,
    },
  });
  // Link to related node if found
  if (dedupeResult.action === 'link' && dedupeResult.existingNode && config.linkRelated) {
    await linkRelatedNode(node.id, dedupeResult.existingNode.id);
    return {
      captured: true,
      action: 'linked',
      node,
      reason: `linked to related node (similarity: ${(dedupeResult.similarity! * 100).toFixed(1)}%)`,
    };
  }
  return {
    captured: true,
    action: 'created',
    node,
  };
 }
 export async function captureText(
  text: string,
  options: { tags?: string[]; source?: string } = {}
 ): Promise<CaptureResult> {
  const config = getCaptureConfig();
  if (config.mode === 'off') {
    return { captured: false, action: 'skipped', reason: 'capture disabled' };
  }
  // Simple text capture - no summarization needed
  const dedupeResult = await checkDuplicate(text, text);
  const tags = ['manual-capture', ...(options.tags || [])];
  if (options.source) {
    tags.push(`source:${options.source}`);
  }
  if (dedupeResult.action === 'merge' && dedupeResult.existingNode) {
    const merged = await mergeIntoNode(
      dedupeResult.existingNode.id,
      text.slice(0, 100),
      text,
      tags
    );
    return {
      captured: true,
      action: 'merged',
      node: merged || undefined,
    };
  }
  const node = await addNode({
    kind: 'memory',
    title: text.slice(0, 100),
    content: text,
    tags,
    status: 'active',
    metadata: {
      source: options.source || 'manual',
      capturedAt: Date.now(),
    },
  });
  if (dedupeResult.action === 'link' && dedupeResult.existingNode && config.linkRelated) {
    await linkRelatedNode(node.id, dedupeResult.existingNode.id);
    return { captured: true, action: 'linked', node };
  }
  return { captured: true, action: 'created', node };
 }
--- a/src/core/capture/summarize.ts
+++ b/src/core/capture/summarize.ts
@@ -0,0 +1,160 @@
 import { generate, isGenAvailable } from '../search/ollamaGen';
 export interface ExtractedMemory {
  summary: string;
  topics: string[];
  decisions: string[];
  filesDiscussed: string[];
 }
 const SUMMARIZE_PROMPT = `Summarize this Claude Code conversation in 1-2 sentences.
 Focus on: what was accomplished, decisions made, problems solved.
 Do NOT include greetings or meta-discussion.
 Conversation:
 {conversation}
 Summary:`;
 const EXTRACT_PROMPT = `Extract from this conversation:
 1. Main topics (as tags, lowercase, hyphenated, max 5)
 2. Decisions made (if any, max 3)
 3. Code files discussed or modified (if any)
 Conversation:
 {conversation}
 Output as JSON only, no explanation:
 {"topics": [], "decisions": [], "files": []}`;
 export async function summarizeConversation(conversation: string): Promise<string | null> {
  if (!(await isGenAvailable())) return null;
  const prompt = SUMMARIZE_PROMPT.replace('{conversation}', conversation);
  return generate(prompt);
 }
 export async function extractMemoryData(conversation: string): Promise<ExtractedMemory | null> {
  const available = await isGenAvailable();
  // Get summary
  const summary = available
    ? await summarizeConversation(conversation)
    : createFallbackSummary(conversation);
  if (!summary) return null;
  // Extract structured data
  let topics: string[] = [];
  let decisions: string[] = [];
  let filesDiscussed: string[] = [];
  if (available) {
    const extractPrompt = EXTRACT_PROMPT.replace('{conversation}', conversation);
    const extracted = await generate(extractPrompt);
    if (extracted) {
      try {
        // Find JSON in response (handle cases where model adds explanation)
        const jsonMatch = extracted.match(/\{[\s\S]*\}/);
        if (jsonMatch) {
          const data = JSON.parse(jsonMatch[0]);
          topics = Array.isArray(data.topics) ? data.topics.slice(0, 5) : [];
          decisions = Array.isArray(data.decisions) ? data.decisions.slice(0, 3) : [];
          filesDiscussed = Array.isArray(data.files) ? data.files : [];
        }
      } catch {
        // Fall back to basic extraction
        topics = extractTopicsBasic(conversation);
        filesDiscussed = extractFilesBasic(conversation);
      }
    }
  } else {
    // Basic extraction without AI
    topics = extractTopicsBasic(conversation);
    filesDiscussed = extractFilesBasic(conversation);
  }
  return {
    summary,
    topics: sanitizeTags(topics),
    decisions,
    filesDiscussed,
  };
 }
 function createFallbackSummary(conversation: string): string {
  // Take first meaningful line as summary
  const lines = conversation.split('\n').filter(l => l.trim().length > 20);
  if (lines.length === 0) return 'Conversation captured';
  const first = lines[0].trim();
  return first.length > 150 ? first.slice(0, 147) + '...' : first;
 }
 function extractTopicsBasic(conversation: string): string[] {
  const topics: string[] = [];
  const lower = conversation.toLowerCase();
  // Common programming topics
  const keywords = [
    'typescript', 'javascript', 'python', 'rust', 'go',
    'react', 'vue', 'angular', 'node', 'express',
    'database', 'sql', 'api', 'auth', 'authentication',
    'bug', 'fix', 'error', 'refactor', 'test', 'deploy',
    'git', 'docker', 'kubernetes', 'aws', 'cloud',
  ];
  for (const kw of keywords) {
    if (lower.includes(kw) && topics.length < 5) {
      topics.push(kw);
    }
  }
  return topics;
 }
 function extractFilesBasic(conversation: string): string[] {
  const files: string[] = [];
  // Match file paths
  const filePatterns = [
    /[\w\-\/]+\.(ts|js|tsx|jsx|py|rs|go|md|json|yaml|yml|toml|sql)/gi,
    /src\/[\w\-\/]+/gi,
  ];
  for (const pattern of filePatterns) {
    const matches = conversation.match(pattern);
    if (matches) {
      for (const m of matches) {
        if (!files.includes(m) && files.length < 10) {
          files.push(m);
        }
      }
    }
  }
  return files;
 }
 function sanitizeTags(tags: string[]): string[] {
  return tags
    .map(t => t.toLowerCase().trim().replace(/\s+/g, '-').replace(/[^a-z0-9\-]/g, ''))
    .filter(t => t.length > 0 && t.length < 30);
 }
 export function shouldCapture(conversation: string, minLength: number): boolean {
  // Skip very short conversations
  if (conversation.length < minLength) return false;
  // Skip if mostly greetings/pleasantries
  const lower = conversation.toLowerCase();
  const greetings = ['hello', 'hi ', 'hey', 'thanks', 'thank you', 'goodbye', 'bye'];
  const greetingCount = greetings.filter(g => lower.includes(g)).length;
  // If more than half the "content" is greetings, skip
  const words = conversation.split(/\s+/).length;
  if (words < 20 && greetingCount > 2) return false;
  return true;
 }
--- a/src/core/config.ts
+++ b/src/core/config.ts
@@ -1,119 +0,0 @@
 import { getDb } from './db';
 export interface CortexConfig {
  // Context injection settings
  'context.maxTokens': number;
  'context.maxNodes': number;
  'context.includeRecent': boolean;
  'context.includeProject': boolean;
  'context.includeTasks': boolean;
  'context.includeDecisions': boolean;
 }
 const DEFAULTS: CortexConfig = {
  'context.maxTokens': 4000,
  'context.maxNodes': 20,
  'context.includeRecent': true,
  'context.includeProject': true,
  'context.includeTasks': true,
  'context.includeDecisions': true,
 };
 /**
 * Ensure the config table exists
 */
 function ensureConfigTable(): void {
  const db = getDb();
  db.exec(`
    CREATE TABLE IF NOT EXISTS config (
      key TEXT PRIMARY KEY,
      value TEXT NOT NULL,
      updated_at INTEGER NOT NULL
    )
  `);
 }
 /**
 * Get a config value
 */
 export function getConfig<K extends keyof CortexConfig>(key: K): CortexConfig[K] {
  ensureConfigTable();
  const db = getDb();
  const row = db.prepare('SELECT value FROM config WHERE key = ?').get(key) as { value: string } | undefined;
  if (!row) {
    return DEFAULTS[key];
  }
  // Parse based on expected type
  const defaultValue = DEFAULTS[key];
  if (typeof defaultValue === 'boolean') {
    return (row.value === 'true') as unknown as CortexConfig[K];
  }
  if (typeof defaultValue === 'number') {
    return parseInt(row.value, 10) as unknown as CortexConfig[K];
  }
  return row.value as unknown as CortexConfig[K];
 }
 /**
 * Set a config value
 */
 export function setConfig<K extends keyof CortexConfig>(key: K, value: CortexConfig[K]): void {
  ensureConfigTable();
  const db = getDb();
  const now = Date.now();
  const strValue = String(value);
  db.prepare(`
    INSERT INTO config (key, value, updated_at)
    VALUES (?, ?, ?)
    ON CONFLICT(key) DO UPDATE SET value = ?, updated_at = ?
  `).run(key, strValue, now, strValue, now);
 }
 /**
 * List all config values
 */
 export function listConfig(): Array<{ key: string; value: string; isDefault: boolean }> {
  ensureConfigTable();
  const db = getDb();
  const rows = db.prepare('SELECT key, value FROM config').all() as Array<{ key: string; value: string }>;
  const stored = new Map(rows.map(r => [r.key, r.value]));
  const result: Array<{ key: string; value: string; isDefault: boolean }> = [];
  for (const [key, defaultValue] of Object.entries(DEFAULTS)) {
    const storedValue = stored.get(key);
    if (storedValue !== undefined) {
      result.push({ key, value: storedValue, isDefault: false });
    } else {
      result.push({ key, value: String(defaultValue), isDefault: true });
    }
  }
  return result;
 }
 /**
 * Reset a config key to default
 */
 export function resetConfig(key: keyof CortexConfig): void {
  ensureConfigTable();
  const db = getDb();
  db.prepare('DELETE FROM config WHERE key = ?').run(key);
 }
 /**
 * Get context config as a structured object
 */
 export function getContextConfig() {
  return {
    maxTokens: getConfig('context.maxTokens'),
    maxNodes: getConfig('context.maxNodes'),
    includeRecent: getConfig('context.includeRecent'),
    includeProject: getConfig('context.includeProject'),
    includeTasks: getConfig('context.includeTasks'),
    includeDecisions: getConfig('context.includeDecisions'),
  };
 }
--- a/src/core/context.ts
+++ b/src/core/context.ts
@@ -1,291 +0,0 @@
 import { getDb } from './db';
 import { query, listNodes } from './store';
 import { Node, NodeKind } from '../types';
 import { getContextConfig } from './config';
 export interface RankedNode {
  node: Node;
  score: number;
  reason: 'recent' | 'project' | 'task' | 'decision' | 'semantic';
 }
 export interface ContextConfig {
  maxTokens: number;
  maxNodes: number;
  includeRecent: boolean;
  includeProject: boolean;
  includeTasks: boolean;
  includeDecisions: boolean;
 }
 export const DEFAULT_CONTEXT_CONFIG: ContextConfig = {
  maxTokens: 4000,
  maxNodes: 20,
  includeRecent: true,
  includeProject: true,
  includeTasks: true,
  includeDecisions: true,
 };
 /**
 * Get nodes accessed within the last N hours
 */
 export function getRecentNodes(hours: number = 48, limit: number = 10): Node[] {
  const db = getDb();
  const cutoff = Date.now() - hours * 60 * 60 * 1000;
  const rows = db.prepare(`
    SELECT * FROM nodes
    WHERE is_stale = 0 AND last_accessed_at > ?
    ORDER BY last_accessed_at DESC
    LIMIT ?
  `).all(cutoff, limit) as any[];
  return rows.map(rowToNode);
 }
 /**
 * Get nodes tagged with a specific project name
 */
 export function getProjectNodes(projectName: string, limit: number = 10): Node[] {
  return listNodes({ tags: [projectName.toLowerCase()], limit });
 }
 /**
 * Get open tasks (status: todo, in_progress, or active)
 */
 export function getOpenTasks(limit: number = 10): Node[] {
  const db = getDb();
  const rows = db.prepare(`
    SELECT * FROM nodes
    WHERE is_stale = 0
      AND kind = 'task'
      AND (status = 'todo' OR status = 'in_progress' OR status = 'active' OR status IS NULL)
    ORDER BY updated_at DESC
    LIMIT ?
  `).all(limit) as any[];
  return rows.map(rowToNode);
 }
 /**
 * Get recent decisions
 */
 export function getRecentDecisions(limit: number = 5): Node[] {
  return listNodes({ kind: 'decision', limit });
 }
 /**
 * Get semantic matches for a query
 */
 export async function getSemanticMatches(queryText: string, limit: number = 10): Promise<RankedNode[]> {
  const results = await query(queryText, { limit });
  return results.map(r => ({
    node: r.node,
    score: r.score,
    reason: 'semantic' as const,
  }));
 }
 /**
 * Estimate token count for a node (rough approximation)
 */
 function estimateTokens(node: Node): number {
  const text = `${node.title} ${node.content || ''} ${node.tags.join(' ')}`;
  // Rough estimate: 1 token ≈ 4 characters
  return Math.ceil(text.length / 4);
 }
 /**
 * Deduplicate and rank nodes, keeping highest score per node
 */
 function dedupeAndRank(candidates: RankedNode[]): RankedNode[] {
  const byId = new Map<string, RankedNode>();
  for (const c of candidates) {
    const existing = byId.get(c.node.id);
    if (!existing || c.score > existing.score) {
      byId.set(c.node.id, c);
    }
  }
  return Array.from(byId.values()).sort((a, b) => b.score - a.score);
 }
 /**
 * Select nodes within token budget
 */
 function selectWithinBudget(candidates: RankedNode[], maxTokens: number, maxNodes: number): RankedNode[] {
  const selected: RankedNode[] = [];
  let totalTokens = 0;
  for (const c of candidates) {
    if (selected.length >= maxNodes) break;
    const tokens = estimateTokens(c.node);
    if (totalTokens + tokens > maxTokens) continue;
    selected.push(c);
    totalTokens += tokens;
  }
  return selected;
 }
 /**
 * Group nodes by their reason
 */
 function groupByReason(nodes: RankedNode[]): Record<string, RankedNode[]> {
  const groups: Record<string, RankedNode[]> = {};
  for (const n of nodes) {
    if (!groups[n.reason]) groups[n.reason] = [];
    groups[n.reason].push(n);
  }
  return groups;
 }
 /**
 * Format a single node for context output
 */
 function formatNode(ranked: RankedNode): string {
  const n = ranked.node;
  const lines: string[] = [];
  lines.push(`### ${n.title}`);
  if (n.content) {
    // Truncate long content
    const content = n.content.length > 500 ? n.content.slice(0, 500) + '...' : n.content;
    lines.push(content);
  }
  if (n.tags.length) {
    lines.push(`*Tags: ${n.tags.join(', ')}*`);
  }
  return lines.join('\n');
 }
 /**
 * Format context as markdown
 */
 export function formatContext(nodes: RankedNode[]): string {
  if (nodes.length === 0) {
    return '*No relevant context found.*';
  }
  const groups = groupByReason(nodes);
  const sections: string[] = [];
  // Order: project > decisions > tasks > recent > semantic
  const order: Array<{ key: string; title: string }> = [
    { key: 'project', title: 'Project Context' },
    { key: 'decision', title: 'Key Decisions' },
    { key: 'task', title: 'Open Tasks' },
    { key: 'recent', title: 'Recent Activity' },
    { key: 'semantic', title: 'Related Memories' },
  ];
  for (const { key, title } of order) {
    const group = groups[key];
    if (group?.length) {
      sections.push(`## ${title}\n\n${group.map(formatNode).join('\n\n')}`);
    }
  }
  return sections.join('\n\n---\n\n');
 }
 /**
 * Main context gathering function
 */
 export async function gatherContext(
  options: {
    project?: string;
    semanticQuery?: string;
    config?: Partial<ContextConfig>;
  } = {}
 ): Promise<{ nodes: RankedNode[]; formatted: string }> {
  // Load stored config, then override with any passed options
  const storedConfig = getContextConfig();
  const config = { ...storedConfig, ...options.config };
  const candidates: RankedNode[] = [];
  // 1. Project-specific nodes (highest priority)
  if (config.includeProject && options.project) {
    const projectNodes = getProjectNodes(options.project, 10);
    candidates.push(...projectNodes.map(node => ({
      node,
      score: 0.95,
      reason: 'project' as const,
    })));
  }
  // 2. Recent decisions
  if (config.includeDecisions) {
    const decisions = getRecentDecisions(5);
    candidates.push(...decisions.map(node => ({
      node,
      score: 0.85,
      reason: 'decision' as const,
    })));
  }
  // 3. Open tasks
  if (config.includeTasks) {
    const tasks = getOpenTasks(5);
    candidates.push(...tasks.map(node => ({
      node,
      score: 0.80,
      reason: 'task' as const,
    })));
  }
  // 4. Recent activity
  if (config.includeRecent) {
    const recent = getRecentNodes(48, 10);
    candidates.push(...recent.map(node => ({
      node,
      score: 0.70,
      reason: 'recent' as const,
    })));
  }
  // 5. Semantic search on project context
  if (options.semanticQuery) {
    const semantic = await getSemanticMatches(options.semanticQuery, 10);
    // Scale semantic scores to fit our priority scheme
    candidates.push(...semantic.map(r => ({
      ...r,
      score: r.score * 0.6, // Max 0.6 for semantic matches
    })));
  }
  // Dedupe, rank, and select within budget
  const ranked = dedupeAndRank(candidates);
  const selected = selectWithinBudget(ranked, config.maxTokens, config.maxNodes);
  return {
    nodes: selected,
    formatted: formatContext(selected),
  };
 }
 // Helper to convert DB row to Node (duplicated from store.ts to avoid circular deps)
 function rowToNode(row: any): Node {
  return {
    id: row.id,
    kind: row.kind,
    title: row.title,
    content: row.content,
    status: row.status ?? undefined,
    tags: JSON.parse(row.tags || '[]'),
    metadata: JSON.parse(row.metadata || '{}'),
    embedding: null, // Don't load embeddings for context
    createdAt: row.created_at,
    updatedAt: row.updated_at,
    lastAccessedAt: row.last_accessed_at ?? row.updated_at,
    isStale: !!row.is_stale,
  };
 }
--- a/src/mcp/index.ts
+++ b/src/mcp/index.ts
@@ -367,37 +367,6 @@ server.tool(
  }
 );
 // --- memory_context ---
 import { gatherContext, DEFAULT_CONTEXT_CONFIG } from '../core/context';
 server.tool(
  'memory_context',
  'Get relevant context for a Claude session. Gathers recent activity, project-specific nodes, open tasks, and decisions. Use at session start.',
  {
    project: z.string().optional().describe('Project name to filter by (e.g. "cortex")'),
    query: z.string().optional().describe('Optional semantic search query'),
    maxTokens: z.number().optional().describe(`Max tokens in output (default ${DEFAULT_CONTEXT_CONFIG.maxTokens})`),
    maxNodes: z.number().optional().describe(`Max nodes to include (default ${DEFAULT_CONTEXT_CONFIG.maxNodes})`),
  },
  async ({ project, query: semanticQuery, maxTokens, maxNodes }) => {
    const result = await gatherContext({
      project,
      semanticQuery,
      config: {
        maxTokens: maxTokens ?? DEFAULT_CONTEXT_CONFIG.maxTokens,
        maxNodes: maxNodes ?? DEFAULT_CONTEXT_CONFIG.maxNodes,
      },
    });
    return {
      content: [{
        type: 'text' as const,
        text: result.formatted,
      }],
    };
  }
 );
 // --- memory_summary ---
 import { getCachedSummary, generateSummary } from '../core/summary';
@@ -416,6 +385,69 @@ server.tool(
  }
 );
 // --- memory_capture ---
 import { captureConversation, captureText, getCaptureConfig, setCaptureConfig, CaptureMode } from '../core/capture';
 server.tool(
  'memory_capture',
  'Capture a conversation or context as a memory node. Uses AI to summarize and extract key information.',
  {
    conversation: z.string().describe('The conversation or context to capture'),
    sessionId: z.string().optional().describe('Session identifier'),
    filesChanged: z.array(z.string()).optional().describe('List of files that were changed'),
    source: z.string().optional().describe('Source identifier (default: claude-code)'),
  },
  async ({ conversation, sessionId, filesChanged, source }) => {
    const result = await captureConversation({
      conversation,
      sessionId,
      filesChanged,
      source: source || 'claude-code',
    });
    return { content: [{ type: 'text' as const, text: serialize(result) }] };
  }
 );
 server.tool(
  'memory_remember',
  'Remember a piece of text for later. Simpler than memory_capture - for quick notes and facts.',
  {
    text: z.string().describe('The text to remember'),
    tags: z.array(z.string()).optional().describe('Tags to apply'),
  },
  async ({ text, tags }) => {
    const result = await captureText(text, { tags, source: 'remember' });
    return { content: [{ type: 'text' as const, text: serialize(result) }] };
  }
 );
 server.tool(
  'memory_capture_config',
  'Get or set auto-capture configuration',
  {
    action: z.enum(['get', 'set']).describe('Action to perform'),
    mode: z.enum(['always', 'manual', 'decisions', 'off']).optional().describe('Capture mode (for set)'),
    minLength: z.number().optional().describe('Minimum conversation length (for set)'),
    autoTag: z.boolean().optional().describe('Auto-generate tags (for set)'),
    linkRelated: z.boolean().optional().describe('Auto-link related nodes (for set)'),
  },
  async ({ action, mode, minLength, autoTag, linkRelated }) => {
    if (action === 'get') {
      const config = getCaptureConfig();
      return { content: [{ type: 'text' as const, text: serialize(config) }] };
    }
    const updates: Partial<{ mode: CaptureMode; minLength: number; autoTag: boolean; linkRelated: boolean }> = {};
    if (mode !== undefined) updates.mode = mode;
    if (minLength !== undefined) updates.minLength = minLength;
    if (autoTag !== undefined) updates.autoTag = autoTag;
    if (linkRelated !== undefined) updates.linkRelated = linkRelated;
    const config = setCaptureConfig(updates);
    return { content: [{ type: 'text' as const, text: serialize({ updated: true, config }) }] };
  }
 );
 // --- memory_prompt ---
 import { interpretAndExecute } from '../core/prompt/interpreter';
--- a/src/server/routes.ts
+++ b/src/server/routes.ts
@@ -4,7 +4,6 @@ import { getConnections, buildTree } from '../core/graph';
 import { getDb } from '../core/db';
 import { determineGroupingStrategy, groupResults } from './queryOrganizer';
 import { getLastReport, markDirty, runMaintenance } from './heartbeat';
 import { gatherContext } from '../core/context';
 const router = Router();
@@ -167,42 +166,6 @@ router.post('/maintenance/run', async (_req: Request, res: Response) => {
  }
 });
 // Context — get session context for Claude
 router.get('/context', async (req: Request, res: Response) => {
  try {
    const project = req.query.project as string | undefined;
    const semanticQuery = req.query.query as string | undefined;
    const maxTokens = req.query.maxTokens ? parseInt(req.query.maxTokens as string) : undefined;
    const maxNodes = req.query.maxNodes ? parseInt(req.query.maxNodes as string) : undefined;
    const format = req.query.format as string || 'markdown';
    const result = await gatherContext({
      project,
      semanticQuery,
      config: { maxTokens, maxNodes } as any,
    });
    if (format === 'json') {
      res.json({
        project,
        nodeCount: result.nodes.length,
        nodes: result.nodes.map(r => ({
          id: r.node.id,
          kind: r.node.kind,
          title: r.node.title,
          score: r.score,
          reason: r.reason,
        })),
        formatted: result.formatted,
      });
    } else {
      res.type('text/markdown').send(result.formatted);
    }
  } catch (err: any) {
    res.status(500).json({ error: err.message });
  }
 });
 // Prompt — AI-driven natural language instruction
 router.post('/prompt', async (req: Request, res: Response) => {
  try {