private.xml

<?xml version="1.0"?>
<root>
  <!-- ============================================================ -->
  <!-- appdef for microsoft remote desktop -->
  <appdef>
    <appname>MSREMOTEDESKTOP</appname>
    <equal>com.microsoft.rdc.mac</equal>
  </appdef>

  <item>
    <name>Swap Option and Command on Microsoft Remote Desktop</name>
    <identifier>private.appdef</identifier>
    <only>MSREMOTEDESKTOP</only>
    <autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::OPTION_L</autogen>
    <autogen>__KeyToKey__ KeyCode::COMMAND_R, KeyCode::OPTION_R</autogen>
  </item>
  <!-- ============================================================ -->
</root>