fix(github): persist GitHub indexer data between CLI invocations

packages/cli/src/commands/gh.ts

@@ -3,7 +3,6 @@
  * CLI commands for indexing and searching GitHub data
  */
 
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
 import { GitHubIndexer } from '@lytics/dev-agent-subagents';
 import chalk from 'chalk';
 import { Command } from 'commander';
@@ -34,12 +33,15 @@ export const ghCommand = new Command('gh')
 
           spinner.text = 'Initializing indexers...';
 
-          // Initialize code indexer
-          const codeIndexer = new RepositoryIndexer(config);
-          await codeIndexer.initialize();
+          // Create GitHub indexer with vector storage
+          const ghIndexer = new GitHubIndexer({
+            vectorStorePath: `${config.vectorStorePath}-github`, // Separate storage for GitHub data
+            statePath: '.dev-agent/github-state.json',
+            autoUpdate: true,
+            staleThreshold: 15 * 60 * 1000, // 15 minutes
+          });
 
-          // Create GitHub indexer
-          const ghIndexer = new GitHubIndexer(codeIndexer);
+          await ghIndexer.initialize();
 
           spinner.text = 'Fetching GitHub data...';
 
@@ -120,10 +122,14 @@ export const ghCommand = new Command('gh')
 
           spinner.text = 'Initializing...';
 
-          // Initialize indexers
-          const codeIndexer = new RepositoryIndexer(config);
-          await codeIndexer.initialize();
-          const ghIndexer = new GitHubIndexer(codeIndexer);
+          // Initialize GitHub indexer
+          const ghIndexer = new GitHubIndexer({
+            vectorStorePath: `${config.vectorStorePath}-github`,
+            statePath: '.dev-agent/github-state.json',
+            autoUpdate: true,
+            staleThreshold: 15 * 60 * 1000,
+          });
+          await ghIndexer.initialize();
 
           // Check if indexed
           if (!ghIndexer.isIndexed()) {
@@ -216,9 +222,13 @@ export const ghCommand = new Command('gh')
 
           spinner.text = 'Initializing...';
 
-          const codeIndexer = new RepositoryIndexer(config);
-          await codeIndexer.initialize();
-          const ghIndexer = new GitHubIndexer(codeIndexer);
+          const ghIndexer = new GitHubIndexer({
+            vectorStorePath: `${config.vectorStorePath}-github`,
+            statePath: '.dev-agent/github-state.json',
+            autoUpdate: true,
+            staleThreshold: 15 * 60 * 1000,
+          });
+          await ghIndexer.initialize();
 
           if (!ghIndexer.isIndexed()) {
             spinner.warn('GitHub data not indexed');
@@ -301,9 +311,13 @@ export const ghCommand = new Command('gh')
           return;
         }
 
-        const codeIndexer = new RepositoryIndexer(config);
-        await codeIndexer.initialize();
-        const ghIndexer = new GitHubIndexer(codeIndexer);
+        const ghIndexer = new GitHubIndexer({
+          vectorStorePath: `${config.vectorStorePath}-github`,
+          statePath: '.dev-agent/github-state.json',
+          autoUpdate: true,
+          staleThreshold: 15 * 60 * 1000,
+        });
+        await ghIndexer.initialize();
 
         const stats = ghIndexer.getStats();
 

packages/cli/src/index.ts

@@ -1,4 +1,4 @@
-import { CoreService, type CoreConfig } from '@lytics/dev-agent-core';
+import { type CoreConfig, CoreService } from '@lytics/dev-agent-core';
 
 export interface CliConfig {
   coreConfig: CoreConfig;

packages/core/src/context/index.ts

@@ -5,7 +5,6 @@ export interface ContextProviderOptions {
 }
 
 export class ContextProvider {
-
   constructor(_options: ContextProviderOptions) {
     // Placeholder constructor
   }

packages/core/src/github/index.ts

@@ -4,7 +4,6 @@ export interface GitHubOptions {
 }
 
 export class GitHubIntegration {
-
   constructor(_options: GitHubOptions) {
     // Placeholder constructor
   }

packages/subagents/src/coordinator/github-coordinator.integration.test.ts

@@ -6,40 +6,58 @@
 import { mkdtemp, rm } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
-import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
 import type { GitHubAgentConfig } from '../github/agent';
 import { GitHubAgent } from '../github/agent';
-import type { GitHubContextRequest, GitHubContextResult } from '../github/types';
+import type { GitHubContextRequest, GitHubContextResult, GitHubDocument } from '../github/types';
 import { SubagentCoordinator } from './coordinator';
 
+// Mock GitHub utilities to avoid actual gh CLI calls
+vi.mock('../github/utils/index', () => ({
+  fetchAllDocuments: vi.fn(() => [
+    {
+      type: 'issue',
+      number: 1,
+      title: 'Test Issue',
+      body: 'Test body',
+      state: 'open',
+      author: 'testuser',
+      labels: [],
+      createdAt: '2024-01-01T00:00:00Z',
+      updatedAt: '2024-01-01T00:00:00Z',
+      url: 'https://github.com/test/repo/issues/1',
+      relatedIssues: [],
+      relatedPRs: [],
+      linkedFiles: [],
+      mentions: [],
+    },
+  ]),
+  enrichDocument: vi.fn((doc: GitHubDocument) => doc),
+  getCurrentRepository: vi.fn(() => 'lytics/dev-agent'),
+  calculateRelevance: vi.fn(() => 0.8),
+  matchesQuery: vi.fn(() => true),
+}));
+
 describe('Coordinator → GitHub Integration', () => {
   let coordinator: SubagentCoordinator;
   let github: GitHubAgent;
   let tempDir: string;
-  let codeIndexer: RepositoryIndexer;
 
   beforeEach(async () => {
     // Create temp directory
     tempDir = await mkdtemp(join(tmpdir(), 'gh-coordinator-test-'));
 
-    // Initialize code indexer
-    codeIndexer = new RepositoryIndexer({
-      repositoryPath: process.cwd(),
-      vectorStorePath: join(tempDir, '.vectors'),
-    });
-    await codeIndexer.initialize();
-
     // Create coordinator
     coordinator = new SubagentCoordinator({
       logLevel: 'error', // Reduce noise in tests
     });
 
-    // Create GitHub agent
+    // Create GitHub agent with vector storage config
     const config: GitHubAgentConfig = {
       repositoryPath: process.cwd(),
-      codeIndexer,
-      storagePath: join(tempDir, '.github-index'),
+      vectorStorePath: join(tempDir, '.github-vectors'),
+      statePath: join(tempDir, 'github-state.json'),
+      autoUpdate: false, // Disable for tests
     };
     github = new GitHubAgent(config);
 
@@ -49,7 +67,6 @@ describe('Coordinator → GitHub Integration', () => {
 
   afterEach(async () => {
     await coordinator.stop();
-    await codeIndexer.close();
     await rm(tempDir, { recursive: true, force: true });
   });
 
@@ -67,7 +84,7 @@ describe('Coordinator → GitHub Integration', () => {
     it('should prevent duplicate registration', async () => {
       const duplicate = new GitHubAgent({
         repositoryPath: process.cwd(),
-        codeIndexer,
+        vectorStorePath: join(tempDir, '.github-vectors-dup'),
       });
       await expect(coordinator.registerAgent(duplicate)).rejects.toThrow('already registered');
     });
@@ -101,6 +118,17 @@ describe('Coordinator → GitHub Integration', () => {
     });
 
     it('should route search request to GitHub agent', async () => {
+      // Index first (required for search)
+      await coordinator.sendMessage({
+        type: 'request',
+        sender: 'test',
+        recipient: 'github',
+        payload: {
+          action: 'index',
+          indexOptions: {},
+        } as GitHubContextRequest,
+      });
+
       const response = await coordinator.sendMessage({
         type: 'request',
         sender: 'test',

packages/subagents/src/github/agent.ts

@@ -3,7 +3,6 @@
  * Provides rich context from GitHub issues, PRs, and discussions
  */
 
-import type { RepositoryIndexer } from '@lytics/dev-agent-core';
 import type { Agent, AgentContext, Message } from '../types';
 import { GitHubIndexer } from './indexer';
 import type {
@@ -15,8 +14,10 @@ import type {
 
 export interface GitHubAgentConfig {
   repositoryPath: string;
-  codeIndexer: RepositoryIndexer;
-  storagePath?: string;
+  vectorStorePath: string; // Path to LanceDB storage for GitHub data
+  statePath?: string; // Path to state file (default: .dev-agent/github-state.json)
+  autoUpdate?: boolean; // Enable auto-updates (default: true)
+  staleThreshold?: number; // Stale threshold in ms (default: 15 minutes)
 }
 
 export class GitHubAgent implements Agent {
@@ -35,7 +36,17 @@ export class GitHubAgent implements Agent {
     this.context = context;
     this.name = context.agentName;
 
-    this.indexer = new GitHubIndexer(this.config.codeIndexer, this.config.repositoryPath);
+    this.indexer = new GitHubIndexer(
+      {
+        vectorStorePath: this.config.vectorStorePath,
+        statePath: this.config.statePath,
+        autoUpdate: this.config.autoUpdate,
+        staleThreshold: this.config.staleThreshold,
+      },
+      this.config.repositoryPath
+    );
+
+    await this.indexer.initialize();
 
     context.logger.info('GitHub agent initialized', {
       capabilities: this.capabilities,
@@ -69,10 +80,18 @@ export class GitHubAgent implements Agent {
           result = await this.handleSearch(request.query || '', request.searchOptions);
           break;
         case 'context':
-          result = await this.handleGetContext(request.issueNumber!);
+          if (typeof request.issueNumber !== 'number') {
+            result = { action: 'context', error: 'issueNumber is required' };
+          } else {
+            result = await this.handleGetContext(request.issueNumber);
+          }
           break;
         case 'related':
-          result = await this.handleFindRelated(request.issueNumber!);
+          if (typeof request.issueNumber !== 'number') {
+            result = { action: 'related', error: 'issueNumber is required' };
+          } else {
+            result = await this.handleFindRelated(request.issueNumber);
+          }
           break;
         default:
           result = {
@@ -114,7 +133,8 @@ export class GitHubAgent implements Agent {
   }
 
   private async handleIndex(options?: GitHubIndexOptions): Promise<GitHubContextResult> {
-    const stats = await this.indexer!.index(options);
+    if (!this.indexer) throw new Error('Indexer not initialized');
+    const stats = await this.indexer.index(options);
     return {
       action: 'index',
       stats,
@@ -125,23 +145,26 @@ export class GitHubAgent implements Agent {
     query: string,
     options?: { limit?: number }
   ): Promise<GitHubContextResult> {
-    const results = await this.indexer!.search(query, options);
+    if (!this.indexer) throw new Error('Indexer not initialized');
+    const results = await this.indexer.search(query, options);
     return {
       action: 'search',
       results,
     };
   }
 
   private async handleGetContext(issueNumber: number): Promise<GitHubContextResult> {
-    const context = await this.indexer!.getContext(issueNumber);
+    if (!this.indexer) throw new Error('Indexer not initialized');
+    const context = await this.indexer.getContext(issueNumber);
     return {
       action: 'context',
       context: context || undefined,
     };
   }
 
   private async handleFindRelated(issueNumber: number): Promise<GitHubContextResult> {
-    const related = await this.indexer!.findRelated(issueNumber);
+    if (!this.indexer) throw new Error('Indexer not initialized');
+    const related = await this.indexer.findRelated(issueNumber);
     return {
       action: 'related',
       related,