How can I synchronize the shell view and Finder view of a directory?
This is a known quirk with Finder; it's supposed to refresh automatically, but sometime it's won't.  Unlike Windows, there is no refresh button nor can you press F5 to refresh the window.

There are more details and workarounds to this in the article Refreshing Finder Windows in Mac OS X.  However, I find that the easiest thing is to just go up one directory and then back.  

If you use Keyboard Maestro, you could create a "refresh keystroke" of sorts by mapping a key combo to something like Command Shift A  and then Command [ which will take to you the Applications Folder then back to where you were.