Confused about a bit of code.

http://pastebin.org/121306

Could a friendly soul explain to me why removing/changing the for-loop at line 68-69 changes the whole program?
It changes output from   1 2 3 4 5   to   3 2 1 5 4 
if the input is 5 4 3 2 1

>>6-7
Java has System.arraycopy(src, src_start, dest, dest_start, length).  It's probably the best simple copy function you can implement in the language.