Up until ISE Design Suite 14.2 and Vivado System Generator 2012.2, Vivado System Generator still used the CORE Generator tool in the backend. If using these versions or reviewing design from these versions, you will still see .xco and .cgxco files in the netlist directory.
Starting in Vivado System Generator 2012.3, (coincides with ISE Design Suite System Generator 14.3), this will be tied to the IP Catalog and will no longer use CORE Generator or .xco files. You will see .xci files will be used instead.