How Do You Programmatically Set the Hardware Clock on Linux?

Check out the rtc man-page for details, but if you are logged in as root, something like this:

#include <linux/rtc.h>
#include <sys/ioctl.h>


    struct       rtc_time {
        int         tm_sec;      
        int         tm_min;      
        int         tm_hour;     
        int         tm_mday;     
        int         tm_mon;      
        int         tm_year;     
        int         tm_wday; /* unused */
        int         tm_yday; /* unused */
        int         tm_isdst;/* unused */
    };

int fd;
struct rtc_time rt;
/* set your values here */
fd = open("/dev/rtc", O_RDONLY);
ioctl(fd, RTC_SET_TIME, &rt);
close(fd);

After calling stime(), do this:

system("/sbin/hwclock --systohc");

See the hwclock(8) man page for more information.