AWS an interesting example considering it's also a default search path for the SDK so anything using an AWS SDK is going to check for ~/.aws/config; does boxxy apply the rules to anything run in a shell, or only if 'run by boxxy'?
You may also be able to tell I don't have a lot of AWS experience (:
Boxxy seems good enough for userspace.
Perhaps still too tricky to make it do magic things and break programs in the process, but it could be used to audit who's working with what paths and let the user print a report so they know what apps to boxx up and make them behave.