PHP has simple functions to handle all moving, copying, and deleting files, and quite rightly - they are all very popular things to do, so there is no point making them difficult. If you are using Unix you will know that there is no command for "rename", because renaming a file is essentially the same as moving it, so you use the move (mv) command - it is the same in PHP.
Files are moved using rename(), copied using copy(), and deleted using unlink(). Unlink() might seem like an odd choice of word at first, but Unix systems consider filenames to be "hard links" to the actual files themselves, so to unlink a file is to delete it.
Author's Note: all three functions will operate without further input from you. If you choose to pass an existing file to the second parameter of rename(), it will rename the file in parameter one to the file in parameter two, overwriting the original file. The same applies to copy() - you will overwrite all files without question as long as you have the correct permissions.