It's so insanely easy to get started with puppet or ansible I wouldn't start rolling out a product without using them from the get-go at this point. At the very least properly package your software (read: DEB or RPM, not docker containers) so it's easy to reinstall quickly if need be.
Personally, I like platform libraries rather than OS packages. I have several Ruby projects set up as gems. What's neat about that is it allows code reuse across projects.
So go ahead and vendor them in, outside of inclusion in distribution software packages (with exceptions) there's nothing stopping you from including your own dependencies. Packaging your application properly makes deployment a hell of a lot easier and less error-prone.
