When I use command line tool template it has a bundle identifier inside the wizard. What does bundle identifier mean? Is this similar to namespace?
The bundle identifier is the unique string that identifies your application to the system. This compares to the display name (namespaces are usually prefixes in frameworks), which is what iOS uses to show the name of your app on the springboard.
Bundle identifiers are usually (not always) written out in reverse DNS notation (I.e com.myCompany.myApp).