Toggling switch button to start and pause using logic '0' or '1'

If I correctly understood your needs, you can try changing your code this way:

SIGNAL M: STD_LOGIC;
SIGNAL run: STD_LOGIC;
SIGNAL last_ce: STD_LOGIC;
PROCESS (clock,rst,M)
BEGIN
   IF (rst = '0') THEN
      d1 <= "0000";
	  run <= '0';
	  last_ce <= ce;
   ELSIF (clOCK 'EVENT AND clOCK='1') THEN
      IF (run='1') THEN
          d1<= d1 + '1';
		  M <= '0';
      END IF;
      IF d1= "1001" THEN
         d1<= "0000";
		 M <= '1';
      END IF;
	  IF (ce='1' and last_ce='0')
	      run <= not run;
      END IF;
   END IF;
   clk_2<=M;
END PROCESS;