refactor: enhance directory listing with separate file and directory results

extension/secureflow/packages/secureflow-cli/Dockerfile

@@ -48,9 +48,6 @@ ENV NODE_ENV=production
 ENV TARGETS_FILE=/app/tools/mgmt/targets.txt
 ENV MAX_PLUGINS=50
 
-# Create volume mount points for results and targets file
-VOLUME ["/app/tools/mgmt/results", "/app/tools/mgmt/targets.txt"]
-
 # Set default working directory for the script
 WORKDIR /app
 

extension/secureflow/packages/secureflow-cli/docker-compose.yml

@@ -4,13 +4,6 @@ services:
       context: .
       dockerfile: Dockerfile
     container_name: secureflow-plugin-analyzer
-    volumes:
-      # Mount the targets.txt file (read-only)
-      - ./tools/mgmt/targets.txt:/app/tools/mgmt/targets.txt:ro
-      # Mount results directory for output (read-write)
-      - ./results:/app/tools/mgmt/results:rw
-      # Mount settings directory for API key configuration
-      - secureflow-settings:/home/secureflow/.secureflow
     environment:
       - MAX_PLUGINS=50
       - NODE_ENV=production

extension/secureflow/packages/secureflow-cli/lib/prompts/common/security-review-cli.txt

@@ -61,6 +61,7 @@ You are a highly experienced security engineer conducting a thorough code review
 6. ALWAYS use tools to navigate through the code to understand the complete context of the vulnerability.
    - Even though the project structure is provided, use list files tool to navigate through the code to understand the complete context of the vulnerability.
    - Use file request tool to request for files if needed for complete analysis iteratively.
+   - Always start with list files tool to navigate through the code to understand the complete context of the vulnerability.
 
 Strictly don't report below category of vulnerabilities from Analysis:
    - Theoretical vulnerabilities without practical impact

extension/secureflow/packages/secureflow-cli/lib/prompts/tools/list-file-request-instructions.txt

@@ -1,17 +1,30 @@
 ------
-2. Tool: list files in directory (equivalent to 'ls' command)
-Description: This method helps to list files in a directory
+2. Tool: Directory Listing (List Files and Subdirectories)
+Description: Explore directory contents to discover files and subdirectories for security analysis
+Purpose: Use this tool to navigate the project structure and identify files that need security review
+
 Format:
-<list_file_request path="./relative/path/to/directory" reason="short reason for requesting this directory" />
+<list_file_request path="./relative/path/to/directory" reason="brief explanation of why you need to explore this directory" />
+
+When to use this tool:
+- Start security analysis by exploring the project root directory first
+- Navigate into subdirectories to understand the project structure
+- Discover configuration files, source code files, and security-relevant directories
+- Find entry points, authentication modules, database connections, and API endpoints
+- Explore directories mentioned in build files or configuration
+
+Best practices:
+1. Always start with the root directory (path="./") to get an overview
+2. Use relative paths from the project root (e.g., "./src", "./config", "./api")
+3. Explore directories systematically - start broad, then go deeper
+4. Focus on security-relevant directories like src/, config/, auth/, api/, admin/
+5. Limit to 3-5 directory requests per iteration to avoid overwhelming context
+6. Don't request the same directory multiple times
+7. Skip hidden directories (starting with .) unless they contain configuration files
+8. Prioritize directories that likely contain business logic and security controls
 
-Rules for file requests:
-1. Use relative paths from the project root
-2. Provide a short reason for each request
-3. Files outside project scope will be ignored
-4. Request only directory listed in 'Files in the project' section
-5. Limit to 5 directories per request
-6. Do not request same directory multiple times
-7. Skip directories that were not found previously
-8. Skip non-source directories
-9. Follow project structure strictly
+Example usage sequence:
+1. <list_file_request path="./" reason="Get project overview and identify main directories" />
+2. <list_file_request path="./src" reason="Explore source code structure" />
+3. <list_file_request path="./config" reason="Check configuration files for security settings" />
 ----

extension/secureflow/packages/secureflow-cli/scanner/ai-security-analyzer.js

@@ -181,11 +181,24 @@ class AISecurityAnalyzer {
         if (result.status === 'success') {
           context += `\n=== DIRECTORY: ${result.path} ===\n`;
           context += `Reason: ${result.reason}\n`;
-          context += `Files and directories found (${result.fileCount} items):\n`;
-          result.files.forEach(file => {
-            const icon = file.type === 'directory' ? '📁' : '📄';
-            context += `${icon} ${file.name} (${file.type})\n`;
-          });
+          context += `Total items: ${result.totalCount} (${result.directoryCount} directories, ${result.fileCount} files)\n`;
+
+          // List directories first
+          if (result.directories && result.directories.length > 0) {
+            context += `\nDirectories:\n`;
+            result.directories.forEach(dir => {
+              context += `📁 ${dir.name} (path: ${dir.relativePath})\n`;
+            });
+          }
+
+          // Then list files
+          if (result.files && result.files.length > 0) {
+            context += `\nFiles:\n`;
+            result.files.forEach(file => {
+              context += `📄 ${file.name} (path: ${file.relativePath})\n`;
+            });
+          }
+
           context += `=== END DIRECTORY: ${result.path} ===\n`;
         } else {
           context += `❌ Directory listing failed for ${result.path}: ${result.reason}\n`;
@@ -210,7 +223,7 @@ class AISecurityAnalyzer {
       context += `\n[DIRECTORY LISTING RESULTS]\n`;
       listResults.forEach(result => {
         if (result.status === 'success') {
-          context += `✅ ${result.path}: Successfully listed (${result.fileCount} items)\n`;
+          context += `✅ ${result.path}: Successfully listed (${result.totalCount} total items: ${result.directoryCount} directories, ${result.fileCount} files)\n`;
         } else {
           context += `❌ Directory listing failed for ${result.path}: ${result.reason}. Don't request it again\n`;
         }

extension/secureflow/packages/secureflow-cli/scanner/file-request-handler.js

@@ -241,15 +241,19 @@ class FileRequestHandler {
       }
 
       // List directory contents
-      const files = await this._listDirectoryContents(fullPath);
+      const contents = await this._listDirectoryContents(fullPath);
 
       return {
         status: 'success',
         path: requestedPath,
         fullPath,
-        files,
+        files: contents.files,
+        directories: contents.directories,
+        all: contents.all,
         reason,
-        fileCount: files.length
+        fileCount: contents.files.length,
+        directoryCount: contents.directories.length,
+        totalCount: contents.all.length
       };
 
     } catch (error) {
@@ -263,48 +267,63 @@ class FileRequestHandler {
   }
 
   /**
-   * List directory contents with filtering
+   * List directory contents with filtering, including both files and directories with full paths
    */
   async _listDirectoryContents(dirPath) {
     const { readdir } = require('fs').promises;
 
     try {
       const items = await readdir(dirPath, { withFileTypes: true });
-      const files = [];
+      const result = {
+        files: [],
+        directories: [],
+        all: []
+      };
 
       for (const item of items) {
-        // Skip hidden files and directories
-        if (item.name.startsWith('.') && item.name !== '.env' && item.name !== '.gitignore') {
+        // Skip hidden files and directories (except important config files)
+        if (item.name.startsWith('.') && 
+            item.name !== '.env' && 
+            item.name !== '.gitignore' && 
+            item.name !== '.config' &&
+            item.name !== '.npmrc' &&
+            item.name !== '.dockerignore') {
           continue;
         }
 
         const itemPath = path.join(dirPath, item.name);
         const relativePath = path.relative(this.projectPath, itemPath);
+        const fullPath = path.resolve(itemPath);
+
+        const itemInfo = {
+          name: item.name,
+          type: item.isDirectory() ? 'directory' : 'file',
+          relativePath: relativePath.startsWith('.') ? relativePath : `./${relativePath}`,
+          fullPath: fullPath
+        };
 
         if (item.isDirectory()) {
-          files.push({
-            name: item.name,
-            type: 'directory',
-            relativePath: relativePath
-          });
+          result.directories.push(itemInfo);
         } else if (item.isFile()) {
-          files.push({
-            name: item.name,
-            type: 'file',
-            relativePath: relativePath
-          });
+          result.files.push(itemInfo);
         }
+
+        result.all.push(itemInfo);
       }
 
       // Sort by type (directories first) then by name
-      files.sort((a, b) => {
+      const sortFn = (a, b) => {
         if (a.type !== b.type) {
           return a.type === 'directory' ? -1 : 1;
         }
         return a.name.localeCompare(b.name);
-      });
+      };
+
+      result.files.sort(sortFn);
+      result.directories.sort(sortFn);
+      result.all.sort(sortFn);
 
-      return files;
+      return result;
     } catch (error) {
       throw new Error(`Failed to read directory: ${error.message}`);
     }