feat: Complete GitHub App authentication, documentation generation, and test improvements

- Implement GitHub App authentication (Octokit) with fallback to personal access token
- Add @octokit/auth-app and @octokit/rest dependencies for secure GitHub API access
- Update GitHubService to use Octokit instead of axios for better API compatibility
- Create DocGeneratorAgent for auto-generating project documentation
- Add docs API endpoints for project, file, and README documentation
- Improve scanner report formatting with better issue presentation
- Update server startup logging with environment info and health check URL
- Add error handling for server startup failures
- Create comprehensive test suite (test-ai-agent.js) for CI/CD validation
- Update GitHub Actions workflow to use environment secrets
- Update installation guide with both token auth methods
- Add GitHub App setup instructions to INSTALLATION.md
- Fix environment configuration to support both auth methods

.env.example

@@ -7,6 +7,11 @@ HF_USERNAME=NLarchive
 HF_SPACE_NAME=my-webapp-hf
 GITHUB_BRANCH=main
 
+# GitHub App Authentication (for AI Agent)
+GH_APP_ID=your_github_app_id
+GH_APP_PRIVATE_KEY_B64=your_base64_encoded_private_key
+GH_APP_INSTALLATION_ID=your_installation_id
+
 # Optional
 DRY_RUN=false
 FORCE_PUSH=false

.github/workflows/sync-to-hf.yml

@@ -33,9 +33,11 @@ jobs:
       - name: Push to Hugging Face Space
         env:
           HF_TOKEN: ${{ secrets.HF_TOKEN }}
+          HF_USERNAME: ${{ secrets.HF_USERNAME }}
+          HF_SPACE_NAME: ${{ secrets.HF_SPACE_NAME }}
         run: |
           # Add space remote (ignore if exists)
-          git remote add space https://NLarchive:[email protected]/spaces/NLarchive/my-webapp-hf || true
+          git remote add space https://$HF_USERNAME:[email protected]/spaces/$HF_USERNAME/$HF_SPACE_NAME || true
 
           # Force push to the space
-          git push --force https://NLarchive:[email protected]/spaces/NLarchive/my-webapp-hf main
+          git push --force https://$HF_USERNAME:[email protected]/spaces/$HF_USERNAME/$HF_SPACE_NAME main

public/.env.example

@@ -10,11 +10,18 @@
 # Get from: https://makersuite.google.com/app/apikey
 GEMINI_API_KEY=your_gemini_api_key_here
 
-# GitHub Personal Access Token
+# GitHub Authentication (Choose ONE method)
+# Option 1: Personal Access Token (Simple)
 # Get from: https://github.com/settings/tokens
 # Required scopes: repo, issues, actions
 GITHUB_TOKEN=your_github_token_here
 
+# Option 2: GitHub App (Recommended for production)
+# Get from: https://github.com/settings/apps
+GH_APP_ID=your_github_app_id
+GH_APP_PRIVATE_KEY_B64=your_base64_encoded_private_key
+GH_APP_INSTALLATION_ID=your_app_installation_id
+
 # Hugging Face Token
 # Get from: https://huggingface.co/settings/tokens
 HF_TOKEN=your_huggingface_token_here

public/INSTALLATION.md

@@ -78,7 +78,9 @@ Visit: http://localhost:3000
 4. Paste into .env GEMINI_API_KEY=
 ```
 
-#### 2. GitHub Personal Access Token
+#### 2. GitHub Authentication (Choose One)
+
+**Option A: Personal Access Token (Simple)**
 ```
 1. Go: https://github.com/settings/tokens
 2. Click "Generate new token" → "Generate new token (classic)"
@@ -91,6 +93,41 @@ Visit: http://localhost:3000
 6. Paste into .env GITHUB_TOKEN=
 ```
 
+**Option B: GitHub App (Recommended for Production)**
+```
+1. Go: https://github.com/settings/apps
+2. Click "New GitHub App"
+3. Configure:
+   - Name: "AI Agent HF"
+   - Homepage URL: https://huggingface.co/spaces/YourUsername/your-space
+   - Webhook URL: Leave empty
+   - Permissions:
+     ✓ Repository permissions → Contents: Read & write
+     ✓ Repository permissions → Issues: Read & write
+     ✓ Repository permissions → Pull requests: Read & write
+     ✓ Repository permissions → Actions: Read & write
+     ✓ Repository permissions → Metadata: Read
+4. Generate private key (download .pem file)
+5. Install app on your repository
+6. Get installation ID from app settings
+7. Convert private key to base64:
+   ```bash
+   # On Windows PowerShell
+   [Convert]::ToBase64String([IO.File]::ReadAllBytes("path\to\private-key.pem"))
+   ```
+8. Configure .env:
+   ```
+   GH_APP_ID=your_app_id
+   GH_APP_PRIVATE_KEY_B64=your_base64_private_key
+   GH_APP_INSTALLATION_ID=your_installation_id
+   ```
+9. Test authentication:
+   ```bash
+   cd scripts
+   node test-github-auth.js
+   ```
+```
+
 #### 3. Hugging Face Token
 ```
 1. Go: https://huggingface.co/settings/tokens

public/package-lock.json

@@ -9,6 +9,8 @@
       "version": "1.0.0",
       "dependencies": {
         "@google/generative-ai": "^0.7.0",
+        "@octokit/auth-app": "^6.0.3",
+        "@octokit/rest": "^20.0.2",
         "axios": "^1.6.0",
         "body-parser": "^1.20.2",
         "cors": "^2.8.5",
@@ -30,6 +32,265 @@
         "node": ">=18.0.0"
       }
     },
+    "node_modules/@octokit/auth-app": {
+      "version": "6.1.4",
+      "resolved": "https://registry.npmjs.org/@octokit/auth-app/-/auth-app-6.1.4.tgz",
+      "integrity": "sha512-QkXkSOHZK4dA5oUqY5Dk3S+5pN2s1igPjEASNQV8/vgJgW034fQWR16u7VsNOK/EljA00eyjYF5mWNxWKWhHRQ==",
+      "dependencies": {
+        "@octokit/auth-oauth-app": "^7.1.0",
+        "@octokit/auth-oauth-user": "^4.1.0",
+        "@octokit/request": "^8.3.1",
+        "@octokit/request-error": "^5.1.0",
+        "@octokit/types": "^13.1.0",
+        "deprecation": "^2.3.1",
+        "lru-cache": "npm:@wolfy1339/lru-cache@^11.0.2-patch.1",
+        "universal-github-app-jwt": "^1.1.2",
+        "universal-user-agent": "^6.0.0"
+      },
+      "engines": {
+        "node": ">= 18"
+      }
+    },
+    "node_modules/@octokit/auth-oauth-app": {
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+        "@octokit/types": "^13.0.0",
+        "@types/btoa-lite": "^1.0.0",
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+        "universal-user-agent": "^6.0.0"
+      },
+      "engines": {
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+      }
+    },
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+    },
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+        "@octokit/openapi-types": "^24.2.0"
+      }
+    },
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+    "node_modules/@types/jsonwebtoken": {
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+      "dependencies": {
+        "@types/ms": "*",
+        "@types/node": "*"
+      }
+    },
+    "node_modules/@types/ms": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/@types/ms/-/ms-2.1.0.tgz",
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+    },
+    "node_modules/@types/node": {
+      "version": "24.10.1",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-24.10.1.tgz",
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+      "dependencies": {
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+      }
+    },
     "node_modules/accepts": {
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@@ -81,6 +342,11 @@
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       "dev": true
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+    "node_modules/before-after-hook": {
+      "version": "2.2.3",
+      "resolved": "https://registry.npmjs.org/before-after-hook/-/before-after-hook-2.2.3.tgz",
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+    },
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@@ -138,6 +404,16 @@
         "node": ">=8"
       }
     },
+    "node_modules/btoa-lite": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/btoa-lite/-/btoa-lite-1.0.0.tgz",
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+    },
+    "node_modules/buffer-equal-constant-time": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/buffer-equal-constant-time/-/buffer-equal-constant-time-1.0.1.tgz",
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+    },
     "node_modules/bytes": {
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@@ -282,6 +558,11 @@
         "node": ">= 0.8"
       }
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+    "node_modules/deprecation": {
+      "version": "2.3.1",
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@@ -315,6 +596,14 @@
         "node": ">= 0.4"
       }
     },
+    "node_modules/ecdsa-sig-formatter": {
+      "version": "1.0.11",
+      "resolved": "https://registry.npmjs.org/ecdsa-sig-formatter/-/ecdsa-sig-formatter-1.0.11.tgz",
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+      "dependencies": {
+        "safe-buffer": "^5.0.1"
+      }
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       "resolved": "https://registry.npmjs.org/ee-first/-/ee-first-1.1.1.tgz",
@@ -718,6 +1007,95 @@
         "node": ">=0.12.0"
       }
     },
+    "node_modules/jsonwebtoken": {
+      "version": "9.0.2",
+      "resolved": "https://registry.npmjs.org/jsonwebtoken/-/jsonwebtoken-9.0.2.tgz",
+      "integrity": "sha512-PRp66vJ865SSqOlgqS8hujT5U4AOgMfhrwYIuIhfKaoSCZcirrmASQr8CX7cUg+RMih+hgznrjp99o+W4pJLHQ==",
+      "dependencies": {
+        "jws": "^3.2.2",
+        "lodash.includes": "^4.3.0",
+        "lodash.isboolean": "^3.0.3",
+        "lodash.isinteger": "^4.0.4",
+        "lodash.isnumber": "^3.0.3",
+        "lodash.isplainobject": "^4.0.6",
+        "lodash.isstring": "^4.0.1",
+        "lodash.once": "^4.0.0",
+        "ms": "^2.1.1",
+        "semver": "^7.5.4"
+      },
+      "engines": {
+        "node": ">=12",
+        "npm": ">=6"
+      }
+    },
+    "node_modules/jsonwebtoken/node_modules/ms": {
+      "version": "2.1.3",
+      "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
+      "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA=="
+    },
+    "node_modules/jwa": {
+      "version": "1.4.2",
+      "resolved": "https://registry.npmjs.org/jwa/-/jwa-1.4.2.tgz",
+      "integrity": "sha512-eeH5JO+21J78qMvTIDdBXidBd6nG2kZjg5Ohz/1fpa28Z4CcsWUzJ1ZZyFq/3z3N17aZy+ZuBoHljASbL1WfOw==",
+      "dependencies": {
+        "buffer-equal-constant-time": "^1.0.1",
+        "ecdsa-sig-formatter": "1.0.11",
+        "safe-buffer": "^5.0.1"
+      }
+    },
+    "node_modules/jws": {
+      "version": "3.2.2",
+      "resolved": "https://registry.npmjs.org/jws/-/jws-3.2.2.tgz",
+      "integrity": "sha512-YHlZCB6lMTllWDtSPHz/ZXTsi8S00usEV6v1tjq8tOUZzw7DpSDWVXjXDre6ed1w/pd495ODpHZYSdkRTsa0HA==",
+      "dependencies": {
+        "jwa": "^1.4.1",
+        "safe-buffer": "^5.0.1"
+      }
+    },
+    "node_modules/lodash.includes": {
+      "version": "4.3.0",
+      "resolved": "https://registry.npmjs.org/lodash.includes/-/lodash.includes-4.3.0.tgz",
+      "integrity": "sha512-W3Bx6mdkRTGtlJISOvVD/lbqjTlPPUDTMnlXZFnVwi9NKJ6tiAk6LVdlhZMm17VZisqhKcgzpO5Wz91PCt5b0w=="
+    },
+    "node_modules/lodash.isboolean": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/lodash.isboolean/-/lodash.isboolean-3.0.3.tgz",
+      "integrity": "sha512-Bz5mupy2SVbPHURB98VAcw+aHh4vRV5IPNhILUCsOzRmsTmSQ17jIuqopAentWoehktxGd9e/hbIXq980/1QJg=="
+    },
+    "node_modules/lodash.isinteger": {
+      "version": "4.0.4",
+      "resolved": "https://registry.npmjs.org/lodash.isinteger/-/lodash.isinteger-4.0.4.tgz",
+      "integrity": "sha512-DBwtEWN2caHQ9/imiNeEA5ys1JoRtRfY3d7V9wkqtbycnAmTvRRmbHKDV4a0EYc678/dia0jrte4tjYwVBaZUA=="
+    },
+    "node_modules/lodash.isnumber": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/lodash.isnumber/-/lodash.isnumber-3.0.3.tgz",
+      "integrity": "sha512-QYqzpfwO3/CWf3XP+Z+tkQsfaLL/EnUlXWVkIk5FUPc4sBdTehEqZONuyRt2P67PXAk+NXmTBcc97zw9t1FQrw=="
+    },
+    "node_modules/lodash.isplainobject": {
+      "version": "4.0.6",
+      "resolved": "https://registry.npmjs.org/lodash.isplainobject/-/lodash.isplainobject-4.0.6.tgz",
+      "integrity": "sha512-oSXzaWypCMHkPC3NvBEaPHf0KsA5mvPrOPgQWDsbg8n7orZ290M0BmC/jgRZ4vcJ6DTAhjrsSYgdsW/F+MFOBA=="
+    },
+    "node_modules/lodash.isstring": {
+      "version": "4.0.1",
+      "resolved": "https://registry.npmjs.org/lodash.isstring/-/lodash.isstring-4.0.1.tgz",
+      "integrity": "sha512-0wJxfxH1wgO3GrbuP+dTTk7op+6L41QCXbGINEmD+ny/G/eCqGzxyCsh7159S+mgDDcoarnBw6PC1PS5+wUGgw=="
+    },
+    "node_modules/lodash.once": {
+      "version": "4.1.1",
+      "resolved": "https://registry.npmjs.org/lodash.once/-/lodash.once-4.1.1.tgz",
+      "integrity": "sha512-Sb487aTOCr9drQVL8pIxOzVhafOjZN9UU54hiN8PU3uAiSV7lx1yYNpbNmex2PK6dSJoNTSJUUswT651yww3Mg=="
+    },
+    "node_modules/lru-cache": {
+      "name": "@wolfy1339/lru-cache",
+      "version": "11.0.2-patch.1",
+      "resolved": "https://registry.npmjs.org/@wolfy1339/lru-cache/-/lru-cache-11.0.2-patch.1.tgz",
+      "integrity": "sha512-BgYZfL2ADCXKOw2wJtkM3slhHotawWkgIRRxq4wEybnZQPjvAp71SPX35xepMykTw8gXlzWcWPTY31hlbnRsDA==",
+      "engines": {
+        "node": "18 >=18.20 || 20 || >=22"
+      }
+    },
     "node_modules/math-intrinsics": {
       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz",
@@ -895,6 +1273,14 @@
         "node": ">= 0.8"
       }
     },
+    "node_modules/once": {
+      "version": "1.4.0",
+      "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz",
+      "integrity": "sha512-lNaJgI+2Q5URQBkccEKHTQOPaXdUxnZZElQTZY0MFUAuaEqe1E+Nyvgdz/aIyNi6Z9MzO5dv1H8n58/GELp3+w==",
+      "dependencies": {
+        "wrappy": "1"
+      }
+    },
     "node_modules/parseurl": {
       "version": "1.3.3",
       "resolved": "https://registry.npmjs.org/parseurl/-/parseurl-1.3.3.tgz",
@@ -1019,7 +1405,6 @@
       "version": "7.7.3",
       "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.3.tgz",
       "integrity": "sha512-SdsKMrI9TdgjdweUSR9MweHA4EJ8YxHn8DFaDisvhVlUOe4BF1tLD7GAj0lIqWVl+dPb/rExr0Btby5loQm20Q==",
-      "dev": true,
       "bin": {
         "semver": "bin/semver.js"
       },
@@ -1229,6 +1614,25 @@
       "integrity": "sha512-WxONCrssBM8TSPRqN5EmsjVrsv4A8X12J4ArBiiayv3DyyG3ZlIg6yysuuSYdZsVz3TKcTg2fd//Ujd4CHV1iA==",
       "dev": true
     },
+    "node_modules/undici-types": {
+      "version": "7.16.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz",
+      "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw=="
+    },
+    "node_modules/universal-github-app-jwt": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/universal-github-app-jwt/-/universal-github-app-jwt-1.2.0.tgz",
+      "integrity": "sha512-dncpMpnsKBk0eetwfN8D8OUHGfiDhhJ+mtsbMl+7PfW7mYjiH8LIcqRmYMtzYLgSh47HjfdBtrBwIQ/gizKR3g==",
+      "dependencies": {
+        "@types/jsonwebtoken": "^9.0.0",
+        "jsonwebtoken": "^9.0.2"
+      }
+    },
+    "node_modules/universal-user-agent": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/universal-user-agent/-/universal-user-agent-6.0.1.tgz",
+      "integrity": "sha512-yCzhz6FN2wU1NiiQRogkTQszlQSlpWaw8SvVegAc+bDxbzHgh1vX8uIe8OYyMH6DwH+sdTJsgMl36+mSMdRJIQ=="
+    },
     "node_modules/unpipe": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
@@ -1252,6 +1656,11 @@
       "engines": {
         "node": ">= 0.8"
       }
+    },
+    "node_modules/wrappy": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+      "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ=="
     }
   }
 }

public/package.json

@@ -12,6 +12,8 @@
   },
   "dependencies": {
     "@google/generative-ai": "^0.7.0",
+    "@octokit/auth-app": "^6.0.3",
+    "@octokit/rest": "^20.0.2",
     "express": "^4.18.2",
     "axios": "^1.6.0",
     "dotenv": "^16.3.1",

public/src/agents/doc-generator.js

@@ -0,0 +1,122 @@
+/**
+ * Documentation Generator Agent
+ * Auto-generates documentation for project files
+ */
+
+import { projectService } from '../services/project.js';
+import { geminiService } from '../services/gemini.js';
+import { logger } from '../config/logger.js';
+
+class DocGeneratorAgent {
+  /**
+   * Generate documentation for project structure
+   * @param {Object} structure - Project structure
+   * @returns {Promise<string>} Generated documentation
+   */
+  async generateProjectDocumentation(structure) {
+    try {
+      const prompt = `Generate concise documentation for this project structure. Include:
+1. Project overview
+2. Directory structure explanation
+3. Key files purpose
+4. How to get started
+
+Project structure:
+- Files: ${structure.files.map((f) => f.name).join(', ')}
+- Directories: ${structure.directories.map((d) => d.name).join(', ')}`;
+
+      const doc = await geminiService.generate(prompt);
+      return doc;
+    } catch (error) {
+      logger.error('Failed to generate documentation', { error: error.message });
+      throw error;
+    }
+  }
+
+  /**
+   * Generate file-specific documentation
+   * @param {string} filePath - Path to file
+   * @returns {Promise<string>} File documentation
+   */
+  async generateFileDocumentation(filePath) {
+    try {
+      const content = await projectService.getFileContent(filePath);
+      const language = this.getLanguageFromPath(filePath);
+
+      const prompt = `Analyze this ${language} file and generate:
+1. Purpose/Summary
+2. Key functions or exports
+3. Dependencies
+4. Usage example (if applicable)
+
+Code:
+\`\`\`${language}
+${content.substring(0, 2000)}
+\`\`\``;
+
+      const doc = await geminiService.generate(prompt);
+      return doc;
+    } catch (error) {
+      logger.error('Failed to generate file documentation', {
+        error: error.message,
+        file: filePath,
+      });
+      throw error;
+    }
+  }
+
+  /**
+   * Generate README for project
+   * @returns {Promise<string>} Generated README
+   */
+  async generateReadme() {
+    try {
+      const structure = await projectService.getProjectStructure();
+      const keyFiles = structure.files.filter(
+        (f) =>
+          f.name.match(/package\.json|\.env\.example|Dockerfile|docker-compose/i) ||
+          f.name.endsWith('.md')
+      );
+
+      const prompt = `Create a professional README.md for a Node.js AI agent project. Include:
+1. Project title and description
+2. Features
+3. Prerequisites
+4. Installation steps
+5. Configuration (with example .env)
+6. Running the application
+7. API documentation
+8. Architecture overview
+9. Contributing
+10. License
+
+Key files in project: ${keyFiles.map((f) => f.name).join(', ')}`;
+
+      const readme = await geminiService.generate(prompt);
+      return readme;
+    } catch (error) {
+      logger.error('Failed to generate README', { error: error.message });
+      throw error;
+    }
+  }
+
+  /**
+   * Helper: Get language from file path
+   * @param {string} filePath - File path
+   * @returns {string} Language
+   */
+  getLanguageFromPath(filePath) {
+    if (filePath.endsWith('.js')) return 'javascript';
+    if (filePath.endsWith('.ts')) return 'typescript';
+    if (filePath.endsWith('.jsx')) return 'jsx';
+    if (filePath.endsWith('.tsx')) return 'tsx';
+    if (filePath.endsWith('.py')) return 'python';
+    if (filePath.endsWith('.java')) return 'java';
+    if (filePath.endsWith('.go')) return 'go';
+    if (filePath.endsWith('.json')) return 'json';
+    if (filePath.endsWith('.yaml') || filePath.endsWith('.yml')) return 'yaml';
+    return 'text';
+  }
+}
+
+export const docGeneratorAgent = new DocGeneratorAgent();

public/src/agents/scanner.js

@@ -188,14 +188,14 @@ For each suggestion provide:
       const issueBody = this.formatScanReportAsIssue(report);
 
       const issue = await githubService.createIssue({
-        title: `🤖 AI Scanner: Issues Detected`,
+        title: `🤖 AI Scanner: Issues Detected (${new Date().toLocaleDateString()})`,
         body: issueBody,
-        labels: ['ai-detected', 'needs-review'],
+        labels: ['ai-detected', 'needs-review', 'auto-generated'],
       });
 
-      logger.info('Created issue from scan', { issueNumber: issue.number });
+      logger.info('Created issue from scan', { issueNumber: issue.number, repo: config.GITHUB_REPO });
     } catch (error) {
-      logger.error('Failed to create issue', { error: error.message });
+      logger.error('Failed to create issue', { error: error.message, repo: config.GITHUB_REPO });
     }
   }
 
@@ -206,24 +206,39 @@ For each suggestion provide:
    */
   formatScanReportAsIssue(report) {
     let body = '## 🤖 AI Scanner Report\n\n';
+    body += `**Repository:** ${config.GITHUB_REPO}\n`;
+    body += `**Branch:** ${config.GITHUB_BRANCH}\n\n`;
 
     if (report.issues.length > 0) {
-      body += '### Issues Found\n';
+      body += '### 🚨 Issues Found\n';
       report.issues.forEach((issue) => {
         body += `- **[${issue.severity}]** ${issue.message}\n`;
         body += `  - File: \`${issue.file}\`\n`;
         body += `  - Type: ${issue.type}\n\n`;
       });
+    } else {
+      body += '### ✅ No Critical Issues Found\n\n';
     }
 
-    if (report.recommendations.length > 0) {
-      body += '### Recommendations\n';
+    if (report.recommendations && report.recommendations.length > 0) {
+      body += '### 💡 Recommendations\n';
       report.recommendations.forEach((rec) => {
-        body += `- **[${rec.priority}]** ${rec.suggestion}\n`;
+        body += `- **[${rec.priority}]** ${rec.suggestion}\n\n`;
       });
     }
 
-    body += `\n---\n_Scanned at: ${report.timestamp}_\n_Scan duration: ${report.duration}ms_`;
+    if (report.analysis && report.analysis.files.length > 0) {
+      body += '### 📊 Code Analysis\n';
+      report.analysis.files.forEach((f) => {
+        body += `- **${f.name}**: Analyzed successfully\n`;
+      });
+      body += '\n';
+    }
+
+    body += `---\n`;
+    body += `_Scanned at: ${report.timestamp}_\n`;
+    body += `_Scan duration: ${report.duration}ms_\n`;
+    body += `_By: AI Scanner Agent_`;
 
     return body;
   }

public/src/api/docs.js

@@ -0,0 +1,92 @@
+/**
+ * Documentation API Routes
+ * Endpoints for generating project documentation
+ */
+
+import express from 'express';
+import { docGeneratorAgent } from '../agents/doc-generator.js';
+import { projectService } from '../services/project.js';
+import { logger } from '../config/logger.js';
+
+const router = express.Router();
+
+/**
+ * POST /api/docs/project
+ * Generate project documentation
+ */
+router.post('/project', async (req, res) => {
+  try {
+    logger.info('Generating project documentation');
+    const structure = await projectService.getProjectStructure();
+    const doc = await docGeneratorAgent.generateProjectDocumentation(structure);
+
+    res.json({
+      success: true,
+      documentation: doc,
+      timestamp: new Date().toISOString(),
+    });
+  } catch (error) {
+    logger.error('Failed to generate project documentation', { error: error.message });
+    res.status(500).json({
+      error: 'Documentation generation failed',
+      details: error.message,
+    });
+  }
+});
+
+/**
+ * POST /api/docs/file
+ * Generate documentation for a specific file
+ */
+router.post('/file', async (req, res) => {
+  try {
+    const { filePath } = req.body;
+
+    if (!filePath) {
+      return res.status(400).json({
+        error: 'Missing required field: filePath',
+      });
+    }
+
+    logger.info('Generating file documentation', { file: filePath });
+    const doc = await docGeneratorAgent.generateFileDocumentation(filePath);
+
+    res.json({
+      success: true,
+      file: filePath,
+      documentation: doc,
+      timestamp: new Date().toISOString(),
+    });
+  } catch (error) {
+    logger.error('Failed to generate file documentation', { error: error.message });
+    res.status(500).json({
+      error: 'File documentation generation failed',
+      details: error.message,
+    });
+  }
+});
+
+/**
+ * POST /api/docs/readme
+ * Generate README for project
+ */
+router.post('/readme', async (req, res) => {
+  try {
+    logger.info('Generating README');
+    const readme = await docGeneratorAgent.generateReadme();
+
+    res.json({
+      success: true,
+      readme,
+      timestamp: new Date().toISOString(),
+    });
+  } catch (error) {
+    logger.error('Failed to generate README', { error: error.message });
+    res.status(500).json({
+      error: 'README generation failed',
+      details: error.message,
+    });
+  }
+});
+
+export default router;

public/src/config/env.js

@@ -10,9 +10,14 @@ export const config = {
   
   // API Keys
   GEMINI_API_KEY: process.env.GEMINI_API_KEY || '',
-  GITHUB_TOKEN: process.env.GITHUB_TOKEN || '',
+  GITHUB_TOKEN: process.env.GITHUB_TOKEN || '', // Fallback for backward compatibility
   HF_TOKEN: process.env.HF_TOKEN || '',
   
+  // GitHub App Authentication
+  GH_APP_ID: process.env.GH_APP_ID || '',
+  GH_APP_PRIVATE_KEY_B64: process.env.GH_APP_PRIVATE_KEY_B64 || '',
+  GH_APP_INSTALLATION_ID: process.env.GH_APP_INSTALLATION_ID || '',
+  
   // GitHub
   GITHUB_REPO: process.env.GITHUB_REPO || 'NLarchive/my-webapp-hf',
   GITHUB_OWNER: process.env.GITHUB_OWNER || 'NLarchive',
@@ -33,9 +38,17 @@ export const config = {
 };
 
 export function validateConfig() {
-  const required = ['GEMINI_API_KEY', 'GITHUB_TOKEN'];
+  const required = ['GEMINI_API_KEY'];
+  const githubAuth = ['GITHUB_TOKEN', 'GH_APP_ID', 'GH_APP_PRIVATE_KEY_B64', 'GH_APP_INSTALLATION_ID'];
+  
   const missing = required.filter(key => !config[key]);
   
+  // Check if at least one GitHub auth method is configured
+  const hasGitHubAuth = githubAuth.some(key => config[key]);
+  if (!hasGitHubAuth) {
+    missing.push('GitHub authentication (GITHUB_TOKEN or GH_APP_* variables)');
+  }
+  
   if (missing.length > 0) {
     console.error(`Missing required environment variables: ${missing.join(', ')}`);
     process.exit(1);

public/src/server.js

@@ -14,6 +14,7 @@ import { scannerAgent } from './agents/scanner.js';
 import chatRoutes from './api/chat.js';
 import scannerRoutes from './api/scanner.js';
 import projectRoutes from './api/project.js';
+import docsRoutes from './api/docs.js';
 
 const app = express();
 
@@ -41,6 +42,7 @@ app.get('/health', (req, res) => {
 app.use('/api/chat', chatRoutes);
 app.use('/api/scanner', scannerRoutes);
 app.use('/api/project', projectRoutes);
+app.use('/api/docs', docsRoutes);
 
 // Serve static files (HTML, CSS, JS)
 app.use(express.static('.'));
@@ -66,16 +68,25 @@ async function startServer() {
     validateConfig();
 
     // Start server
-    app.listen(config.PORT, () => {
+    const server = app.listen(config.PORT, () => {
       logger.info(`Server started on port ${config.PORT}`);
+      logger.info(`Environment: ${config.NODE_ENV}`);
+      logger.info(`Health check: http://localhost:${config.PORT}/health`);
     });
 
     // Start scanner if enabled
     if (config.ENABLE_AUTO_FIX) {
+      logger.info('Starting periodic scanner...');
       scannerAgent.startPeriodicScanning();
     } else {
-      logger.info('Auto-fix is disabled');
+      logger.info('Auto-fix is disabled (ENABLE_AUTO_FIX=false)');
     }
+
+    // Handle server errors
+    server.on('error', (err) => {
+      logger.error('Server error', { error: err.message });
+      process.exit(1);
+    });
   } catch (error) {
     logger.error('Failed to start server', { error: error.message });
     process.exit(1);

public/src/services/github.js

@@ -3,19 +3,51 @@
  * Handles GitHub API interactions (PR creation, issue creation, commits, etc.)
  */
 
-import axios from 'axios';
+import { Octokit } from '@octokit/rest';
+import { createAppAuth } from '@octokit/auth-app';
 import { config } from '../config/env.js';
 import { logger } from '../config/logger.js';
 
 class GitHubService {
   constructor() {
-    this.api = axios.create({
-      baseURL: 'https://api.github.com',
-      headers: {
-        Authorization: `token ${config.GITHUB_TOKEN}`,
-        Accept: 'application/vnd.github.v3+json',
-      },
-    });
+    this.octokit = null;
+    this.initializeOctokit();
+  }
+
+  async initializeOctokit() {
+    try {
+      // Try GitHub App authentication first
+      if (config.GH_APP_ID && config.GH_APP_PRIVATE_KEY_B64 && config.GH_APP_INSTALLATION_ID) {
+        const privateKey = Buffer.from(config.GH_APP_PRIVATE_KEY_B64, 'base64').toString('utf8');
+
+        const auth = createAppAuth({
+          appId: config.GH_APP_ID,
+          privateKey,
+          installationId: config.GH_APP_INSTALLATION_ID,
+        });
+
+        this.octokit = new Octokit({
+          authStrategy: auth,
+          auth: { type: 'installation' },
+        });
+
+        logger.info('GitHub App authentication initialized');
+      }
+      // Fallback to personal access token
+      else if (config.GITHUB_TOKEN) {
+        this.octokit = new Octokit({
+          auth: config.GITHUB_TOKEN,
+        });
+
+        logger.info('GitHub token authentication initialized');
+      }
+      else {
+        throw new Error('No GitHub authentication method configured');
+      }
+    } catch (error) {
+      logger.error('Failed to initialize GitHub client', { error: error.message });
+      throw error;
+    }
   }
 
   /**
@@ -26,11 +58,15 @@ class GitHubService {
   async createIssue(issue) {
     try {
       const { title, body, labels = [], assignees = [] } = issue;
-      
-      const response = await this.api.post(
-        `/repos/${config.GITHUB_REPO}/issues`,
-        { title, body, labels, assignees }
-      );
+
+      const response = await this.octokit.issues.create({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        title,
+        body,
+        labels,
+        assignees,
+      });
 
       logger.info('GitHub issue created', { issueNumber: response.data.number });
       return response.data;
@@ -55,10 +91,15 @@ class GitHubService {
         draft = false,
       } = pr;
 
-      const response = await this.api.post(
-        `/repos/${config.GITHUB_REPO}/pulls`,
-        { title, body, head, base, draft }
-      );
+      const response = await this.octokit.pulls.create({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        title,
+        body,
+        head,
+        base,
+        draft,
+      });
 
       logger.info('GitHub PR created', { prNumber: response.data.number });
       return response.data;
@@ -75,9 +116,11 @@ class GitHubService {
    */
   async getFileContents(path = '') {
     try {
-      const response = await this.api.get(
-        `/repos/${config.GITHUB_REPO}/contents/${path}`
-      );
+      const response = await this.octokit.repos.getContent({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        path,
+      });
 
       return response.data;
     } catch (error) {
@@ -113,13 +156,13 @@ class GitHubService {
    */
   async triggerWorkflow(workflowId, inputs = {}) {
     try {
-      const response = await this.api.post(
-        `/repos/${config.GITHUB_REPO}/actions/workflows/${workflowId}/dispatches`,
-        {
-          ref: config.GITHUB_BRANCH,
-          inputs,
-        }
-      );
+      const response = await this.octokit.actions.createWorkflowDispatch({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        workflow_id: workflowId,
+        ref: config.GITHUB_BRANCH,
+        inputs,
+      });
 
       logger.info('Workflow triggered', { workflowId });
       return response.data;
@@ -135,7 +178,10 @@ class GitHubService {
    */
   async getRepoInfo() {
     try {
-      const response = await this.api.get(`/repos/${config.GITHUB_REPO}`);
+      const response = await this.octokit.repos.get({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+      });
       return response.data;
     } catch (error) {
       logger.error('Failed to get repo info', { error: error.message });
@@ -150,10 +196,11 @@ class GitHubService {
    */
   async listIssues(state = 'open') {
     try {
-      const response = await this.api.get(
-        `/repos/${config.GITHUB_REPO}/issues`,
-        { params: { state } }
-      );
+      const response = await this.octokit.issues.listForRepo({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        state,
+      });
       return response.data;
     } catch (error) {
       logger.error('Failed to list issues', { error: error.message });
@@ -169,10 +216,12 @@ class GitHubService {
    */
   async addIssueComment(issueNumber, body) {
     try {
-      const response = await this.api.post(
-        `/repos/${config.GITHUB_REPO}/issues/${issueNumber}/comments`,
-        { body }
-      );
+      const response = await this.octokit.issues.createComment({
+        owner: config.GITHUB_OWNER,
+        repo: config.GITHUB_REPO.split('/')[1],
+        issue_number: issueNumber,
+        body,
+      });
 
       logger.info('Issue comment added', { issueNumber });
       return response.data;