Karibiner (aka KeyRemap4MacBook) mapping file

private.xml

<?xml version="1.0"?>
<!-- key modifier file for https://pqrs.org/macosx/keyremap4macbook/ -->
<root>
<appdef> 
    <appname>MacVim</appname> 
    <equal>org.vim.MacVim</equal> 
</appdef> 

<appdef>
    <appname>Iterm2</appname>
    <equal>com.googlecode.iterm2</equal>
</appdef>


<item>
    <name>Swap command and control, except in MacVim and Iterm2</name>
    <identifier>private.swap_command_and_control</identifier>
    <autogen>--KeyToKey-- KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
    <autogen>--KeyToKey-- KeyCode::COMMAND_R, KeyCode::CONTROL_R</autogen>
    <autogen>--KeyToKey-- KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
    <autogen>--KeyToKey-- KeyCode::CONTROL_R, KeyCode::COMMAND_R</autogen>
    <not>MacVim</not>
    <not>Iterm2</not>
  </item>

</root>