Run "newdes2" without any paramaters, and it will show you its command line syntax and options. If you don't know how to run command line programs and piping, please search Google for a tutorial on the Windows Command Prompt. For example, this should encrypt and then decrypt a directory listing:
dir | newdes2 -e -c -u -k mypassword | newdes2 -d -c -u -k mypassword
However, I see some erratic behavior, so good luck finding the bug. Remember that the source code still has obsolete junk such as read() and write(). It may also have problems with text/binary file mode.