Apple is your Sysadmin
/usr is not yours (except for /usr/local).
/System is not yours.
Please, if you are installing your own software or "upgrading". DO NOT PUT IT IN APPLE'S LOCATIONS! If you do, you just broke your operating system. There is a good chance any patch that Apple provides may not work, existing and new software may not work, etc.
If you want to "upgrade" some software or service, put it in /usr/local or /Library. Change your PATH if you need to, maybe something in /etc, but god damnit don't rename, delete, or replace anything in Apple's space! In doing so, you are making your life harder, as well as annoying the heck out of all of us software developers who are writing software that depends on a particular operating system. When you screw with anything that lives on those directories, you are no longer running an operating system that we are willing to support.
/usr/local has been around for decades for this reason. It wouldn't be still be around if it wasn't a better idea than replacing your OS vendor's files on a whim.