Karabiner OSX

private.xml

<?xml version="1.0"?>
<root>

  <windownamedef>
    <name>CODIO_IDE</name>
    <regex>Codio IDE</regex>
  </windownamedef>

  <item>
    <name>Command_L to Control_L</name>
    <appendix>(except Terminal, Virtual Machine, RDC, VNC, TeamViewer, EMACS, X11, Citrix Viewer, Codio IDE)</appendix>
    <identifier>remap.commandL2controlL_extermvm_custom</identifier>
    <not>
      TERMINAL,
      VIRTUALMACHINE,
      REMOTEDESKTOPCONNECTION,
      VNC,
      TEAMVIEWER,
      EMACS,
      X11,
      CITRIX_ONLINE_PLUG_IN,
      CITRIX_XEN_APP_VIEWER,
    </not>
    <windowname_not>
      CODIO_IDE
    </windowname_not>
    <autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
  </item>

  <item>
    <name>Control_L to Command_L</name>
    <appendix>(except Terminal, Virtual Machine, RDC, VNC, TeamViewer, EMACS, X11, Citrix Viewer, Codio IDE)</appendix>
    <identifier>remap.controlL2commandL_extermvm_custom</identifier>
    <not>
      TERMINAL,
      VIRTUALMACHINE,
      REMOTEDESKTOPCONNECTION,
      VNC,
      TEAMVIEWER,
      EMACS,
      X11,
      CITRIX_ONLINE_PLUG_IN,
      CITRIX_XEN_APP_VIEWER,
    </not>
    <windowname_not>
      CODIO_IDE
    </windowname_not>
    <autogen>__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
  </item>
</root>