Apple - How to remove or hide Apple applications from my app folder?

You can hide files from the UI using chflags command. Assuming you want to hide iBooks app, start your terminal app do the following:

$ cd /Applications/
$ sudo chflags hidden iBooks.app

And you are almost done. Start finder app and in Applications folder you won't see iBooks app. But it's still in visible in the Applications Dock folder. You have to restart Dock app, so the last step is to:

$ killall -1 Dock

and you are done!

You won't see the hidden app in the Dock or Finder. It will be visibile to you from the terminal when used ls shell command.

Quick note, to unhide app just use the following command:

$ cd /Applications/
$ sudo chflags nohidden iBooks.app

Notice the nohidden flag. Previously we used hidden

I'd been wondering about this as well. I have my App folder in the side dock which gives me an unwieldy list of names longer than the screen heigth. The solution I tried attacks the problem from another angle.

Instead of cleaning out the App folder, I made a new folder and put in alias's of just the programs I use. You can then drag the folder off to your sidebar and dock and remove the App folder.

This way you still have the App folder in case you have a burning desire to play chess, but in routine use you never have to see it.