fix(filesystem): resolve symlinked allowed directories to both forms

On macOS, /tmp is a symlink to /private/tmp. When users specify /tmp
as an allowed directory, the server was resolving it to /private/tmp
during startup but then rejecting paths like /tmp/file.txt because
they dont start with /private/tmp.

This fix stores BOTH the original normalized path AND the resolved
path in allowedDirectories, so users can access files through either
form. For example, with /tmp as allowed directory, both /tmp/file.txt
and /private/tmp/file.txt will now be accepted.

Fixes #3253

src/filesystem/index.ts

@@ -39,22 +39,32 @@ if (args.length === 0) {
 }
 
 // Store allowed directories in normalized and resolved form
-let allowedDirectories = await Promise.all(
+// We store BOTH the original path AND the resolved path to handle symlinks correctly
+// This fixes the macOS /tmp -> /private/tmp symlink issue where users specify /tmp
+// but the resolved path is /private/tmp
+let allowedDirectories = (await Promise.all(
   args.map(async (dir) => {
     const expanded = expandHome(dir);
     const absolute = path.resolve(expanded);
+    const normalizedOriginal = normalizePath(absolute);
     try {
       // Security: Resolve symlinks in allowed directories during startup
       // This ensures we know the real paths and can validate against them later
       const resolved = await fs.realpath(absolute);
-      return normalizePath(resolved);
+      const normalizedResolved = normalizePath(resolved);
+      // Return both original and resolved paths if they differ
+      // This allows matching against either /tmp or /private/tmp on macOS
+      if (normalizedOriginal !== normalizedResolved) {
+        return [normalizedOriginal, normalizedResolved];
+      }
+      return [normalizedResolved];
     } catch (error) {
       // If we can't resolve (doesn't exist), use the normalized absolute path
       // This allows configuring allowed dirs that will be created later
-      return normalizePath(absolute);
+      return [normalizedOriginal];
     }
   })
-);
+)).flat();
 
 // Validate that all directories exist and are accessible
 await Promise.all(allowedDirectories.map(async (dir) => {