In the past I used something like inotab to use an inotify-based trigger to pipe data from SSH to a different system that didn't have any NAS or SAN support, it might also work to detect 'who' is touching any files that boxxy has previously seen rules for.

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.

For a structured approach to ptrace/syscall rewriting, you could try FB's reverie. I worked on and used it during an internship a few years back; it's pretty amazing at what it does.

https://github.com/facebookexperimental/reverie

Fun fact, one layer of App Engine's sandbox from a couple years ago was implemented using ptrace. It will redirect filesystem IO to in-memory files.