Ubuntu, like many other free operating systems, have a beautiful package management system that will track what depends on what, what is installed, what is not, what is not longer needed, which versions of each. If you tamper with it, you are asking for trouble. If you do a manual upgrade, from sources, eventually a package upgrade will downgrade your version or some other application being incompatible will not work. And once you start throwing files in /usr, you start to ask for trouble. I’ve been using this type of operating systems for years and I’ve learned this by experience.