Altera EP2C5 mini board clock pin

Quartus will work out from your code what signals are clocks and what signals are not clocks. It is good practice to connect your 'clk' signal to a dedicated clock input pin.

A dedicated clock input pin can also be used as a general purpose input pin, for an input signal that is not a clock. That is all that the pin listing is telling you. So, if you were to add an input signal to your example as follows:

module ledblink(
   input  wire clk,
   input  wire stop,
   output wire LED
);
reg  cnt;
always @(posedge clk)
   if (!stop)
      cnt <= cnt + 24'd1;
assign LED = cnt;
endmodule

The input signal 'stop' could connect up to another 'dedicated clock/input' pin or any other user I/O pin.

Cheers,

Alex