feat: add semantic graph design for static code analysis

- Introduced a comprehensive design document for a Code Semantic Graph aimed at enhancing static analysis capabilities.
- Defined the architecture, core components, and implementation steps for analyzing function calls, data flow, and dependencies.
- Included detailed specifications for nodes and edges in the graph, along with database schema for storage.
- Outlined phases for implementation, technical challenges, success metrics, and application scenarios.

ccw/src/core/routes/mcp-routes.ts

@@ -77,7 +77,7 @@ function getMcpServersFromFile(filePath) {
  */
 function addMcpServerToMcpJson(projectPath, serverName, serverConfig) {
   try {
-    const normalizedPath = normalizeProjectPathForConfig(projectPath);
+    const normalizedPath = normalizePathForFileSystem(projectPath);
     const mcpJsonPath = join(normalizedPath, '.mcp.json');
     
     // Read existing .mcp.json or create new structure
@@ -115,7 +115,7 @@ function addMcpServerToMcpJson(projectPath, serverName, serverConfig) {
  */
 function removeMcpServerFromMcpJson(projectPath, serverName) {
   try {
-    const normalizedPath = normalizeProjectPathForConfig(projectPath);
+    const normalizedPath = normalizePathForFileSystem(projectPath);
     const mcpJsonPath = join(normalizedPath, '.mcp.json');
     
     if (!existsSync(mcpJsonPath)) {
@@ -238,22 +238,43 @@ function getMcpConfig() {
 }
 
 /**
- * Normalize project path for .claude.json (Windows backslash format)
+ * Normalize path to filesystem format (for accessing .mcp.json files)
+ * Always uses forward slashes for cross-platform compatibility
  * @param {string} path
  * @returns {string}
  */
-function normalizeProjectPathForConfig(path) {
-  // Convert forward slashes to backslashes for Windows .claude.json format
-  let normalized = path.replace(/\//g, '\\');
-
-  // Handle /d/path format -> D:\path
-  if (normalized.match(/^\\[a-zA-Z]\\/)) {
+function normalizePathForFileSystem(path) {
+  let normalized = path.replace(/\\/g, '/');
+  
+  // Handle /d/path format -> D:/path
+  if (normalized.match(/^\/[a-zA-Z]\//)) {
     normalized = normalized.charAt(1).toUpperCase() + ':' + normalized.slice(2);
   }
-
+  
   return normalized;
 }
 
+/**
+ * Normalize project path to match existing format in .claude.json
+ * Checks both forward slash and backslash formats to find existing entry
+ * @param {string} path
+ * @param {Object} claudeConfig - Optional existing config to check format
+ * @returns {string}
+ */
+function normalizeProjectPathForConfig(path, claudeConfig = null) {
+  // IMPORTANT: Always normalize to forward slashes to prevent duplicate entries
+  // (e.g., prevents both "D:/Claude_dms3" and "D:\\Claude_dms3")
+  let normalizedForward = path.replace(/\\/g, '/');
+
+  // Handle /d/path format -> D:/path
+  if (normalizedForward.match(/^\/[a-zA-Z]\//)) {
+    normalizedForward = normalizedForward.charAt(1).toUpperCase() + ':' + normalizedForward.slice(2);
+  }
+
+  // ALWAYS return forward slash format to prevent duplicates
+  return normalizedForward;
+}
+
 /**
  * Toggle MCP server enabled/disabled
  * @param {string} projectPath
@@ -270,7 +291,7 @@ function toggleMcpServerEnabled(projectPath, serverName, enable) {
     const content = readFileSync(CLAUDE_CONFIG_PATH, 'utf8');
     const config = JSON.parse(content);
 
-    const normalizedPath = normalizeProjectPathForConfig(projectPath);
+    const normalizedPath = normalizeProjectPathForConfig(projectPath, config);
 
     if (!config.projects || !config.projects[normalizedPath]) {
       return { error: `Project not found: ${normalizedPath}` };
@@ -332,7 +353,7 @@ function addMcpServerToProject(projectPath, serverName, serverConfig, useLegacyC
     const content = readFileSync(CLAUDE_CONFIG_PATH, 'utf8');
     const config = JSON.parse(content);
 
-    const normalizedPath = normalizeProjectPathForConfig(projectPath);
+    const normalizedPath = normalizeProjectPathForConfig(projectPath, config);
 
     // Create project entry if it doesn't exist
     if (!config.projects) {
@@ -387,8 +408,8 @@ function addMcpServerToProject(projectPath, serverName, serverConfig, useLegacyC
  */
 function removeMcpServerFromProject(projectPath, serverName) {
   try {
-    const normalizedPath = normalizeProjectPathForConfig(projectPath);
-    const mcpJsonPath = join(normalizedPath, '.mcp.json');
+    const normalizedPathForFile = normalizePathForFileSystem(projectPath);
+    const mcpJsonPath = join(normalizedPathForFile, '.mcp.json');
     
     let removedFromMcpJson = false;
     let removedFromClaudeJson = false;
@@ -409,6 +430,9 @@ function removeMcpServerFromProject(projectPath, serverName) {
       const content = readFileSync(CLAUDE_CONFIG_PATH, 'utf8');
       const config = JSON.parse(content);
 
+      // Get normalized path that matches existing config format
+      const normalizedPath = normalizeProjectPathForConfig(projectPath, config);
+
       if (config.projects && config.projects[normalizedPath]) {
         const projectConfig = config.projects[normalizedPath];
 
@@ -597,11 +621,13 @@ export async function handleMcpRoutes(ctx: RouteContext): Promise<boolean> {
   // API: Copy MCP server to project
   if (pathname === '/api/mcp-copy-server' && req.method === 'POST') {
     handlePostRequest(req, res, async (body) => {
-      const { projectPath, serverName, serverConfig } = body;
+      const { projectPath, serverName, serverConfig, configType } = body;
       if (!projectPath || !serverName || !serverConfig) {
         return { error: 'projectPath, serverName, and serverConfig are required', status: 400 };
       }
-      return addMcpServerToProject(projectPath, serverName, serverConfig);
+      // configType: 'mcp' = use .mcp.json (default), 'claude' = use .claude.json
+      const useLegacyConfig = configType === 'claude';
+      return addMcpServerToProject(projectPath, serverName, serverConfig, useLegacyConfig);
     });
     return true;
   }

ccw/src/core/routes/memory-routes.ts

@@ -733,7 +733,7 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
     }
 
     try {
-      const configPath = join(projectPath, '.claude', 'rules', 'active_memory.md');
+      const configPath = join(projectPath, '.claude', 'CLAUDE.md');
       const configJsonPath = join(projectPath, '.claude', 'active_memory_config.json');
       const enabled = existsSync(configPath);
       let lastSync: string | null = null;
@@ -784,16 +784,12 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
           return;
         }
 
-        const rulesDir = join(projectPath, '.claude', 'rules');
         const claudeDir = join(projectPath, '.claude');
-        const configPath = join(rulesDir, 'active_memory.md');
+        const configPath = join(claudeDir, 'CLAUDE.md');
         const configJsonPath = join(claudeDir, 'active_memory_config.json');
 
         if (enabled) {
           // Enable: Create directories and initial file
-          if (!existsSync(rulesDir)) {
-            mkdirSync(rulesDir, { recursive: true });
-          }
           if (!existsSync(claudeDir)) {
             mkdirSync(claudeDir, { recursive: true });
           }
@@ -803,8 +799,8 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
             writeFileSync(configJsonPath, JSON.stringify(config, null, 2), 'utf-8');
           }
 
-          // Create initial active_memory.md with header
-          const initialContent = `# Active Memory
+          // Create initial CLAUDE.md with header
+          const initialContent = `# CLAUDE.md - Project Memory
 
 > Auto-generated understanding of frequently accessed files.
 > Last updated: ${new Date().toISOString()}
@@ -867,7 +863,7 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
     return true;
   }
 
-  // API: Active Memory - Sync (analyze hot files using CLI and update active_memory.md)
+  // API: Active Memory - Sync (analyze hot files using CLI and update CLAUDE.md)
   if (pathname === '/api/memory/active/sync' && req.method === 'POST') {
     let body = '';
     req.on('data', (chunk: Buffer) => { body += chunk.toString(); });
@@ -882,8 +878,8 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
           return;
         }
 
-        const rulesDir = join(projectPath, '.claude', 'rules');
-        const configPath = join(rulesDir, 'active_memory.md');
+        const claudeDir = join(projectPath, '.claude');
+        const configPath = join(claudeDir, 'CLAUDE.md');
 
         // Get hot files from memory store - with fallback
         let hotFiles: any[] = [];
@@ -903,8 +899,8 @@ Return ONLY valid JSON in this exact format (no markdown, no code blocks, just p
           return isAbsolute(filePath) ? filePath : join(projectPath, filePath);
         }).filter((p: string) => existsSync(p));
 
-        // Build the active memory content header
-        let content = `# Active Memory
+        // Build the CLAUDE.md content header
+        let content = `# CLAUDE.md - Project Memory
 
 > Auto-generated understanding of frequently accessed files using ${tool.toUpperCase()}.
 > Last updated: ${new Date().toISOString()}
@@ -942,14 +938,29 @@ RULES: Be concise. Focus on practical understanding. Include function signatures
           });
 
           if (result.success && result.execution?.output) {
-            // Extract stdout from output object
-            cliOutput = typeof result.execution.output === 'string'
-              ? result.execution.output
-              : result.execution.output.stdout || '';
+            // Extract stdout from output object with proper serialization
+            const output = result.execution.output;
+            if (typeof output === 'string') {
+              cliOutput = output;
+            } else if (output && typeof output === 'object') {
+              // Handle object output - extract stdout or serialize the object
+              if (output.stdout && typeof output.stdout === 'string') {
+                cliOutput = output.stdout;
+              } else if (output.stderr && typeof output.stderr === 'string') {
+                cliOutput = output.stderr;
+              } else {
+                // Last resort: serialize the entire object as JSON
+                cliOutput = JSON.stringify(output, null, 2);
+              }
+            } else {
+              cliOutput = '';
+            }
           }
 
-          // Add CLI output to content
-          content += cliOutput + '\n\n---\n\n';
+          // Add CLI output to content (only if not empty)
+          if (cliOutput && cliOutput.trim()) {
+            content += cliOutput + '\n\n---\n\n';
+          }
 
         } catch (cliErr) {
           // Fallback to basic analysis if CLI fails
@@ -1007,8 +1018,8 @@ RULES: Be concise. Focus on practical understanding. Include function signatures
         }
 
         // Ensure directory exists
-        if (!existsSync(rulesDir)) {
-          mkdirSync(rulesDir, { recursive: true });
+        if (!existsSync(claudeDir)) {
+          mkdirSync(claudeDir, { recursive: true });
         }
 
         // Write the file