There are two ways to run the EDK flow from the command line:
Method 1Use make; XPS relies on make. There is a make file created for each project: "system.make". You can run the make file using the following commands in a Cygwin shell:
make -f system.make [target]
In the above command, "target" is bits, netlist, etc.
Method 2A more user-friendly way to run XPS is using the no-windows option. In a Cygwin shell, run "xps -nw system.xmp". Type "help" at the command prompt. You should now have command-line control of XPS.
For more information, refer to the XPS section in the "Embedded System Tools Reference Manual" accessible at:
http://www.xilinx.com/ise/embedded/edk_docs.htm