Using an include file from a different module
The files[] = declarations are only for classes you want to reference at runtime. The declaration should be in the module using the classes (not some other module).

If that doesnt work, look at the xautoload module for D7. Or, simply put include 'includes/Permissions.inc'; into the top your custom module file using those classes/functions -- if you use Features, that's what features (for D7) does; adds an include for features.inc.