refactor(core,mcp): remove dead code and stale GitHub references

- Rewrite analyzeFileWithDocs to use pure extractors directly
- Delete 3 now-redundant private wrapper methods
- Remove githubStatePath, checkGitHubIndex, githubIndex from health adapter
- Clean up health adapter tests (remove 5 GitHub-specific tests)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: prosdev

packages/core/src/services/pattern-analysis-service.ts

@@ -238,46 +238,37 @@ export class PatternAnalysisService {
   }
 
   /**
-   * Analyze file patterns using pre-scanned documents (faster)
-   *
-   * @param filePath - Relative path from repository root
-   * @param documents - Pre-scanned documents for this file
-   * @returns Pattern analysis results
+   * Analyze file patterns using pre-scanned documents (fallback path).
    */
   private async analyzeFileWithDocs(
     filePath: string,
     documents: Document[]
   ): Promise<FilePatterns> {
-    // Step 1: Get file stats and content
     const fullPath = path.join(this.config.repositoryPath, filePath);
-    const [stat, content] = await Promise.all([fs.stat(fullPath), fs.readFile(fullPath, 'utf-8')]);
+    const [content, stat, testing] = await Promise.all([
+      fs.readFile(fullPath, 'utf-8'),
+      fs.stat(fullPath),
+      this.analyzeTesting(filePath),
+    ]);
 
-    const lines = content.split('\n').length;
+    const signatures = documents
+      .filter((d) => d.type === 'function' || d.type === 'method')
+      .map((d) => d.metadata.signature || '')
+      .filter(Boolean);
 
-    // Step 2: Extract all patterns (using cached documents)
     return {
-      fileSize: {
-        lines,
-        bytes: stat.size,
-      },
-      testing: await this.analyzeTesting(filePath),
-      importStyle: await this.analyzeImportsFromFile(filePath, documents),
-      errorHandling: this.analyzeErrorHandling(content),
-      typeAnnotations: this.analyzeTypes(documents),
+      fileSize: { lines: content.split('\n').length, bytes: stat.size },
+      testing,
+      importStyle: extractImportStyleFromContent(content),
+      errorHandling: extractErrorHandlingFromContent(content),
+      typeAnnotations: extractTypeCoverageFromSignatures(signatures),
     };
   }
 
-  // ========================================================================
-  // Pattern Extractors (MVP: 5 core patterns)
-  // ========================================================================
-
   /**
    * Analyze test coverage for a file
-   *
-   * Checks for co-located test files (*.test.*, *.spec.*)
    */
   private async analyzeTesting(filePath: string): Promise<TestingPattern> {
-    // Skip if already a test file
     if (isTestFile(filePath)) {
       return { hasTest: false };
     }
@@ -289,37 +280,6 @@ export class PatternAnalysisService {
     };
   }
 
-  /**
-   * Analyze import style from documents
-   *
-   * Always uses content analysis for reliability (scanner may not extract imports from all files).
-   */
-  private async analyzeImportsFromFile(
-    filePath: string,
-    _documents: Document[]
-  ): Promise<ImportStylePattern> {
-    const fullPath = path.join(this.config.repositoryPath, filePath);
-    const content = await fs.readFile(fullPath, 'utf-8');
-    return extractImportStyleFromContent(content);
-  }
-
-  /**
-   * Analyze error handling patterns in file content
-   */
-  private analyzeErrorHandling(content: string): ErrorHandlingPattern {
-    return extractErrorHandlingFromContent(content);
-  }
-
-  /**
-   * Analyze type annotation coverage from documents
-   */
-  private analyzeTypes(documents: Document[]): TypeAnnotationPattern {
-    const signatures = documents
-      .filter((d) => d.type === 'function' || d.type === 'method')
-      .map((d) => d.metadata.signature || '');
-    return extractTypeCoverageFromSignatures(signatures);
-  }
-
   // ========================================================================
   // Pattern Comparisons
   // ========================================================================

packages/mcp-server/src/adapters/__tests__/health-adapter.test.ts

@@ -9,7 +9,6 @@ describe('HealthAdapter', () => {
   let testDir: string;
   let vectorStorePath: string;
   let repositoryPath: string;
-  let githubStatePath: string;
   let adapter: HealthAdapter;
   let context: AdapterContext;
   let execContext: ToolExecutionContext;
@@ -19,16 +18,13 @@ describe('HealthAdapter', () => {
     testDir = path.join(os.tmpdir(), `health-adapter-test-${Date.now()}`);
     vectorStorePath = path.join(testDir, 'vectors');
     repositoryPath = path.join(testDir, 'repo');
-    githubStatePath = path.join(testDir, 'github-state.json');
-
     await fs.mkdir(testDir, { recursive: true });
     await fs.mkdir(vectorStorePath, { recursive: true });
     await fs.mkdir(repositoryPath, { recursive: true });
 
     adapter = new HealthAdapter({
       repositoryPath,
       vectorStorePath,
-      githubStatePath,
     });
 
     context = {
@@ -75,16 +71,6 @@ describe('HealthAdapter', () => {
       // Setup: Create git repository
       await fs.mkdir(path.join(repositoryPath, '.git'));
 
-      // Setup: Create GitHub index
-      await fs.writeFile(
-        githubStatePath,
-        JSON.stringify({
-          version: '1.0.0',
-          lastIndexed: new Date().toISOString(),
-          items: [{ id: 1 }, { id: 2 }],
-        })
-      );
-
       const result = await adapter.execute({}, execContext);
 
       expect(result.success).toBe(true);
@@ -95,13 +81,11 @@ describe('HealthAdapter', () => {
       expect(result.data).toContain('HEALTHY');
       expect(result.data).toContain('Vector Storage');
       expect(result.data).toContain('Repository');
-      expect(result.data).toContain('Github Index');
     });
 
     it('should report degraded when components have warnings', async () => {
       // Vector storage is empty (warning)
       // Repository exists but no .git (warning)
-      // No GitHub index
 
       const result = await adapter.execute({}, execContext);
 
@@ -188,67 +172,6 @@ describe('HealthAdapter', () => {
     });
   });
 
-  describe('GitHub Index Check', () => {
-    it('should pass when index is recent', async () => {
-      await fs.writeFile(
-        githubStatePath,
-        JSON.stringify({
-          version: '1.0.0',
-          lastIndexed: new Date().toISOString(),
-          items: [{ id: 1 }, { id: 2 }, { id: 3 }],
-        })
-      );
-
-      const result = await adapter.execute({}, execContext);
-
-      expect(result.success).toBe(true);
-      expect(result.data).toContain('Github Index');
-      expect(result.data).toContain('3 items');
-    });
-
-    it('should warn when index is stale (>24 hours)', async () => {
-      const yesterday = new Date(Date.now() - 25 * 60 * 60 * 1000);
-      await fs.writeFile(
-        githubStatePath,
-        JSON.stringify({
-          version: '1.0.0',
-          lastIndexed: yesterday.toISOString(),
-          items: [{ id: 1 }],
-        })
-      );
-
-      const result = await adapter.execute({}, execContext);
-
-      expect(result.success).toBe(true);
-      expect(result.data).toContain('Github Index');
-      expect(result.data).toContain('old');
-    });
-
-    it('should warn when index file does not exist', async () => {
-      const result = await adapter.execute({}, execContext);
-
-      expect(result.success).toBe(true);
-      expect(result.data).toContain('not accessible');
-    });
-
-    it('should not check GitHub index when not configured', async () => {
-      const adapterWithoutGithub = new HealthAdapter({
-        repositoryPath,
-        vectorStorePath,
-      });
-
-      await adapterWithoutGithub.initialize(context);
-
-      const result = await adapterWithoutGithub.execute({}, execContext);
-
-      expect(result.success).toBe(true);
-      // Github Index section should not appear when not configured
-      expect(result.data).not.toContain('Github Index');
-
-      await adapterWithoutGithub.shutdown();
-    });
-  });
-
   describe('Output Formatting', () => {
     it('should format uptime correctly', async () => {
       // Wait a moment to accumulate uptime
@@ -309,16 +232,6 @@ describe('HealthAdapter', () => {
       await fs.writeFile(path.join(vectorStorePath, 'data.db'), 'test');
       await fs.mkdir(path.join(repositoryPath, '.git'));
 
-      // Add GitHub index to make it fully healthy
-      await fs.writeFile(
-        githubStatePath,
-        JSON.stringify({
-          version: '1.0.0',
-          lastIndexed: new Date().toISOString(),
-          items: [{ id: 1 }],
-        })
-      );
-
       const healthy = await adapter.healthCheck();
 
       expect(healthy).toBe(true);
@@ -334,15 +247,6 @@ describe('HealthAdapter', () => {
   });
 
   describe('Error Handling', () => {
-    it('should handle invalid GitHub state JSON', async () => {
-      await fs.writeFile(githubStatePath, 'invalid json');
-
-      const result = await adapter.execute({}, execContext);
-
-      expect(result.success).toBe(true);
-      expect(result.data).toContain('⚠️');
-    });
-
     it('should handle permission errors gracefully', async () => {
       // This test is platform-dependent, so we'll skip it if we can't set permissions
       if (process.platform !== 'win32') {

packages/mcp-server/src/adapters/built-in/health-adapter.ts

@@ -13,15 +13,13 @@ import { validateArgs } from '../validation.js';
 export interface HealthCheckConfig {
   repositoryPath: string;
   vectorStorePath: string;
-  githubStatePath?: string;
 }
 
 export interface HealthStatus {
   status: 'healthy' | 'degraded' | 'unhealthy';
   checks: {
     vectorStorage: CheckResult;
     repository: CheckResult;
-    githubIndex?: CheckResult;
   };
   timestamp: string;
   uptime: number; // milliseconds
@@ -61,7 +59,7 @@ export class HealthAdapter extends ToolAdapter {
     return {
       name: 'dev_health',
       description:
-        'Check the health status of the dev-agent MCP server and its dependencies (vector storage, repository, GitHub index)',
+        'Check the health status of the dev-agent MCP server and its dependencies (Antfly vector storage, repository access)',
       inputSchema: {
         type: 'object',
         properties: {
@@ -114,20 +112,12 @@ export class HealthAdapter extends ToolAdapter {
   }
 
   private async performHealthChecks(verbose: boolean): Promise<HealthStatus> {
-    const [vectorStorage, repository, githubIndex] = await Promise.all([
+    const [vectorStorage, repository] = await Promise.all([
       this.checkVectorStorage(verbose),
       this.checkRepository(verbose),
-      this.config.githubStatePath ? this.checkGitHubIndex(verbose) : Promise.resolve(undefined),
     ]);
 
-    const checks: HealthStatus['checks'] = {
-      vectorStorage,
-      repository,
-    };
-
-    if (githubIndex) {
-      checks.githubIndex = githubIndex;
-    }
+    const checks: HealthStatus['checks'] = { vectorStorage, repository };
 
     return {
       status: this.getOverallStatus({ checks } as HealthStatus),
@@ -211,59 +201,6 @@ export class HealthAdapter extends ToolAdapter {
     }
   }
 
-  private async checkGitHubIndex(verbose: boolean): Promise<CheckResult> {
-    if (!this.config.githubStatePath) {
-      return {
-        status: 'warn',
-        message: 'GitHub index not configured',
-      };
-    }
-
-    try {
-      const content = await fs.readFile(this.config.githubStatePath, 'utf-8');
-      const state = JSON.parse(content);
-
-      const lastIndexed = state.lastIndexed ? new Date(state.lastIndexed) : null;
-      const itemCount = state.items?.length ?? 0;
-
-      if (!lastIndexed) {
-        return {
-          status: 'warn',
-          message: 'GitHub index exists but has no lastIndexed timestamp',
-          details: verbose ? { path: this.config.githubStatePath } : undefined,
-        };
-      }
-
-      const ageMs = Date.now() - lastIndexed.getTime();
-      const ageHours = Math.floor(ageMs / (1000 * 60 * 60));
-
-      // Warn if index is older than 24 hours
-      if (ageHours > 24) {
-        return {
-          status: 'warn',
-          message: `GitHub index is ${ageHours}h old (${itemCount} items) - consider re-indexing`,
-          details: verbose
-            ? { path: this.config.githubStatePath, lastIndexed: lastIndexed.toISOString() }
-            : undefined,
-        };
-      }
-
-      return {
-        status: 'pass',
-        message: `GitHub index operational (${itemCount} items, indexed ${ageHours}h ago)`,
-        details: verbose
-          ? { path: this.config.githubStatePath, lastIndexed: lastIndexed.toISOString() }
-          : undefined,
-      };
-    } catch (error) {
-      return {
-        status: 'warn',
-        message: `GitHub index not accessible: ${error instanceof Error ? error.message : String(error)}`,
-        details: verbose ? { path: this.config.githubStatePath } : undefined,
-      };
-    }
-  }
-
   private getOverallStatus(health: HealthStatus): 'healthy' | 'degraded' | 'unhealthy' {
     const checks = Object.values(health.checks).filter(
       (check): check is CheckResult => check !== undefined