VaultPress is a WordPress only solution. Your own scripts are custom so I think you'll need to create something custom for them or find a script that does something on the generic side. Keep in mind the more generic something is, the more likely it will have false positives.
Jeff's idea above should work, but again keep in mind that any time someone legitimately changes a file you're going to get an alert. Maybe you'd want to limit how often the script runs or have a way to turn it off when you know work is being done. Or better have it selectively check files so if you know your theme is being worked on you can ignore alerts on those changes (though you'd still want to store the changes for a latter comparison).