Why not start a new project and follow the path from the document above? When you get to the .vhd file(s), you can copy in the ones you have from wherever they are or, better, start over with your PORT blocks matching the .xdc file. It's probably better to match a known good .xdc than to get overly creative.
In the case of the Nexys 4 DDR board, the clock signal has the unfortunate name CLK100MHZ in the .xdc file. I can use that in my .vhd files or I can alias it to 'clk' after I bring it in through the PORT block or I can change the .xdc file to ClkIn which I did above.
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## Clock signal
#set_property -dict { PACKAGE_PIN E3 IOSTANDARD LVCMOS33 } [get_ports { CLK100MHZ }]; #IO_L12P_T1_MRCC_35 Sch=clk100mhz
#create_clock -add -name sys_clk_pin -period 10.00 -waveform {0 5} [get_ports {CLK100MHZ}];
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Just change the two lines substituting your clock name for CLK100MHz
Of course, this is for the Nexys4 DDR, you may not be using that board.