If you call store_commands() method anywhere in my code, execution of the command fails for some reason.
such as my main method
int main (int argc,  char * argv[]) {
        char  *command;
        store_commands(); // problem
        while ( (command = readline(" $ "))!= NULL ) {  // scan stdin  
                rl_bind_key('\t',rl_complete);
                splitCommands(&mainVars, command, argv);   
        }
        return 0;
}
my store commands method
void store_commands() {
        char *newEnv;
        DIR * dir;
        char *new ;          
        struct dirent * entry;
        char *env = getenv("PATH");
        do { 
                newEnv = strsep(&env, ":");
                if(newEnv != NULL) 
                        if(strlen(newEnv) > 0) {
                                dir = opendir(newEnv);
                                if( dir == NULL ) break;
                                if(flag == 1) {
                                        flag = 0;
                                        while((entry = readdir(dir)) != NULL) {
                                                new = malloc(strlen(entry->d_name) + 1) ;  
                                                new = strcpy(new, entry->d_name);
                                                commands[++count] = new;  // add possible commands into an array
                                                //printf("---%i %s\n", count ,commands[count]);
                                        }
                                }
                                closedir(dir); // close directory
                        }
        } while(newEnv);
}
test cases
without store_commands()
**ls**
comm[0]: 'ls' and comm[1]: '(null)' // command received here
Makefile        
main.c                      
target
libedit.2.dylib 
with store_commands()
**ls**
comm[0]: 'ls' and comm[1]: '(null)' // command received here again but....
Execution of the command is failed 
: No such file or directory 
 
    