Two Applications folders, one empty
The Application folder inside your home folder is for apps which are restricted to your user. So some applications choose to "install"
  or copy their application in this folder. It's based on the decision
  of the app creator. But most of the apps are installed in the
  /Applications folder.
  Apple decided to hide the /Users folder. That's it.
  


With this command:

sudo chflags nohidden /Users


unhides it.