Doownloaded the experimental 0.13.0 headless server, extracted it and tried to create a new map:

fac@irs:~$ tar xfz factorio_headless_x64_0.13.0.tar.gz
fac@irs:~$ cd factorio/bin/x64/
fac@irs:~/factorio/bin/x64$ ./factorio --create new-server
0.000 2016-06-28 12:39:09; Factorio 0.13.0 (Build ...