Fix apidoc#55 missing 2 chars in root folder

Author: alisinabh

lib/utils/find_files.js

@@ -135,7 +135,11 @@ FindFiles.prototype.search = function() {
     // remove source path prefix
     if (self.path !== './') {
       files = files.map( function(filename) {
-        return filename.substr(self.path.length);
+        if (filename.startsWith(self.path)) {
+            return filename.substr(self.path.length);
+        } else {
+            return filename;
+        }
       });
     }
   }