Galaxy has had a tool dependency management system for quite a while now, but it was never documented in the past. I have just written this documentation:
The system does not automatically install anything for you (this is something we plan to work on for the Tool Shed that is not yet under way), but explains how Galaxy expects to find dependencies and how you can do more advanced things than setting $PATH, if doing so would be useful for your environment.
The tool_dependency_dir option is not in the universe_wsgi.ini.sample file in the current stable release. I just added it in the development version (galaxy-central), so it'll be part of the next release. However, the code to handle it is part of the stable release (and has been for over a year), so if you add it to your config file, the system will behave as described.