security: path validation, ReDoS prevention, picomatch, PID-based file lock

- Add validateProjectPath() to reject sensitive system directories
- Add isPathWithinRoot/isPathWithinRootReal for symlink-aware path checks
- Replace hand-rolled glob-to-regex with picomatch to prevent ReDoS
- Add isSafeRegex() to reject custom patterns with nested quantifiers
- Replace FileLock with PID-tracking version that detects stale locks
- Add symlink detection in removeDirectory/listDirectoryContents
- Add subdirectory name validation in ensureSubdirectory
- Add atomicWriteFileSync and corrupted file backup in config-writer
- Add MCP input validation (validateString) for all tool handlers
- Fix CLAUDE.md section replacement to handle ### subsections correctly

src/directory.ts

@@ -115,6 +115,20 @@ export function removeDirectory(projectRoot: string): void {
     return;
   }
 
+  // Verify .codegraph is a real directory, not a symlink pointing elsewhere
+  const lstat = fs.lstatSync(codegraphDir);
+  if (lstat.isSymbolicLink()) {
+    // Only remove the symlink itself, never follow it for recursive delete
+    fs.unlinkSync(codegraphDir);
+    return;
+  }
+
+  if (!lstat.isDirectory()) {
+    // Not a directory - remove the single file
+    fs.unlinkSync(codegraphDir);
+    return;
+  }
+
   // Recursively remove directory
   fs.rmSync(codegraphDir, { recursive: true, force: true });
 }
@@ -137,6 +151,11 @@ export function listDirectoryContents(projectRoot: string): string[] {
     for (const entry of entries) {
       const relativePath = prefix ? `${prefix}/${entry.name}` : entry.name;
 
+      // Skip symlinks to prevent following links outside .codegraph
+      if (entry.isSymbolicLink()) {
+        continue;
+      }
+
       if (entry.isDirectory()) {
         walkDir(path.join(dir, entry.name), relativePath);
       } else {
@@ -165,6 +184,11 @@ export function getDirectorySize(projectRoot: string): number {
     const entries = fs.readdirSync(dir, { withFileTypes: true });
 
     for (const entry of entries) {
+      // Skip symlinks to prevent following links outside .codegraph
+      if (entry.isSymbolicLink()) {
+        continue;
+      }
+
       const fullPath = path.join(dir, entry.name);
 
       if (entry.isDirectory()) {
@@ -184,6 +208,10 @@ export function getDirectorySize(projectRoot: string): number {
  * Ensure a subdirectory exists within .codegraph
  */
 export function ensureSubdirectory(projectRoot: string, subdirName: string): string {
+  if (subdirName.includes('..') || subdirName.includes(path.sep) || subdirName.includes('/')) {
+    throw new Error(`Invalid subdirectory name: ${subdirName}`);
+  }
+
   const subdirPath = path.join(getCodeGraphDir(projectRoot), subdirName);
 
   if (!fs.existsSync(subdirPath)) {