Fix implicit function declarations and attempt to free non-heap obj

--- lib/subopt.c
+++ lib/subopt.c
@@ -80,12 +80,12 @@
 #include <string.h>
 #include <math.h>
 #include "fold.h"
+#include "cofold.h"
 #include "utils.h"
 #include "energy_par.h"
 #include "fold_vars.h"
 #include "pair_mat.h"
 #include "list.h"
-#include "subopt.h"
 #include "params.h"
 
 #define true	  1
--- Progs/RNAfold.c
+++ Progs/RNAfold.c
@@ -20,6 +20,7 @@
 #include "MEA.h"
 extern void  read_parameter_file(const char fname[]);
 extern plist * stackProb(double cutoff);
+extern void init_pf_circ_fold(int length);
 
 /*@unused@*/
 static char UNUSED rcsid[] = "$Id: vienna-rna-1.8.4-implicits.patch,v 1.1 2010/10/15 07:15:15 xarthisius Exp $";
--- Cluster/AS_main.c
+++ Cluster/AS_main.c
@@ -1,6 +1,7 @@
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
+#include <unistd.h>
 #include "distance_matrix.h"
 #include "statgeom.h"
 #include "split.h"
@@ -226,7 +227,7 @@
 	    for(j=0;j<nn[i];j++) free(ss[i][j]);
 	    free(ss[i]);
          }
-	 free(ss);
+	 // free(ss); 	//  attempt to free a non-heap object ‘ss’
       }
       else {
          printf_taxa_list();