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In addition to the applications loaded in the PortableApps directory, you can create arbitrary shortcuts to applications in other locations.  If the applications are not found on the system when the menu is created, the shortcut will not be displayed.  You can use the variables '$TRUECRYPTDRIVE$' and '$HOSTDRIVE$' which will be substituted with the appropriate drive letter at runtime.

For example, to create a shortcut to TrueCrypt as installed with geek.menu, enter
$HOSTDRIVE$:\TrueCrypt\TrueCrypt.exe