diff --git a/src/Documentation/Git/Repository.php b/src/Documentation/Git/Repository.php
index bf79370..da94412 100644
--- a/src/Documentation/Git/Repository.php
+++ b/src/Documentation/Git/Repository.php
@@ -3,7 +3,10 @@
 
 namespace Synapse\Documentation\Git;
 
+use RecursiveDirectoryIterator;
+use RecursiveIteratorIterator;
 use RuntimeException;
+use UnexpectedValueException;
 
 /**
  * Represents a git repository for documentation
@@ -103,30 +106,36 @@ public function getMarkdownFiles(): array
             $searchPath .= DS . str_replace('/', DS, $this->root);
         }
 
-        if (!is_dir($searchPath)) {
+        if (!is_dir($searchPath) || !is_readable($searchPath)) {
             return [];
         }
 
-        $command = sprintf(
-            'find %s -type f -name "*.md" 2>/dev/null',
-            escapeshellarg($searchPath),
-        );
-
-        $output = [];
-        exec($command, $output);
-
         $files = [];
         $pathPrefix = $this->path . DS;
         $pathPrefixLen = strlen($pathPrefix);
 
-        foreach ($output as $file) {
-            // Convert absolute path to relative path from repo root
-            if (str_starts_with($file, $pathPrefix)) {
-                $relativePath = substr($file, $pathPrefixLen);
-                // Normalize directory separators
-                $relativePath = str_replace(DS, '/', $relativePath);
-                $files[] = $relativePath;
+        try {
+            $iterator = new RecursiveIteratorIterator(
+                new RecursiveDirectoryIterator(
+                    $searchPath,
+                    RecursiveDirectoryIterator::SKIP_DOTS,
+                ),
+            );
+
+            foreach ($iterator as $file) {
+                if ($file->isFile() && $file->getExtension() === 'md') {
+                    $absolutePath = $file->getPathname();
+                    if (str_starts_with($absolutePath, $pathPrefix)) {
+                        $relativePath = substr($absolutePath, $pathPrefixLen);
+                        $relativePath = str_replace(DS, '/', $relativePath);
+                        $files[] = $relativePath;
+                    }
+                }
             }
+        } catch (UnexpectedValueException $unexpectedValueException) {
+            // Permission denied or unreadable subdirectory encountered
+            // Return files collected so far to allow partial indexing
+            return $files;
         }
 
         return $files;
diff --git a/tests/TestCase/Documentation/Git/RepositoryTest.php b/tests/TestCase/Documentation/Git/RepositoryTest.php
index 116d2ae..a046fb7 100644
--- a/tests/TestCase/Documentation/Git/RepositoryTest.php
+++ b/tests/TestCase/Documentation/Git/RepositoryTest.php
@@ -537,4 +537,35 @@ public function testMultiplePullsTracked(): void
         $repository->pull();
         $this->assertEquals(3, $this->gitAdapter->getPullCount($repoPath));
     }
+
+    /**
+     * Test getMarkdownFiles normalizes path separators to forward slashes
+     *
+     * Verifies that the RecursiveDirectoryIterator implementation returns
+     * paths with forward slashes regardless of the operating system.
+     */
+    public function testGetMarkdownFilesNormalizesPathSeparators(): void
+    {
+        $repoPath = $this->testDir . 'test-repo';
+        mkdir($repoPath . DS . '.git', 0755, true);
+        mkdir($repoPath . DS . 'docs' . DS . 'guides' . DS . 'advanced', 0755, true);
+
+        file_put_contents($repoPath . DS . 'docs' . DS . 'guides' . DS . 'advanced' . DS . 'tips.md', '# Tips');
+
+        $repository = new Repository(
+            url: 'https://github.com/test/repo.git',
+            branch: 'main',
+            path: $repoPath,
+            gitAdapter: $this->gitAdapter,
+        );
+
+        $files = $repository->getMarkdownFiles();
+
+        // All paths should use forward slashes, never backslashes
+        foreach ($files as $file) {
+            $this->assertStringNotContainsString('\\', $file, 'Path should not contain backslashes: ' . $file);
+        }
+
+        $this->assertContains('docs/guides/advanced/tips.md', $files);
+    }
 }