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do not turn on LEDs in machineinit() as it was only for tests.
some cleanup in comments

/*
 * $Id: config.c,v 1.12 2007/11/24 17:45:19 nbrk Exp $
 */
#include <sys/types.h>
#include <sys/device.h>

#include <dev/cpuvar.h>
#include <arch/sam7s64/dev/at91sam7.h>

/*
 * Configuration file for platform (AT91SAM7S64).
 */

/* device drivers */
extern struct driver root_dr;
extern struct driver cpu_dr;
extern struct driver saapbus_dr;
extern struct driver sapio_dr;
extern struct driver gpioled_dr;


extern void 	(*putchar)(char);
extern void 	sausart_early_putchar(char ch);

/* amount of physical memory, in Bytes */
uint32_t physmem = 16384 /* 16KB :) */;

/*
 * Where to attach each device.
 */
struct attachinfo config_attachinfo[] = {
	/* child,   parent, pminor, loc, 	intrno, flags */
	{ "cpu" , 	"root", 	0, 0, 			0,	0 },
	{ "saapbus","root", 	0, 0, 			0,	0 },
	{ "sapio",  "saapbus", 	0, 0, 			0,  0 },
	{ "gpioled","sapio", 	0, 17, 			0, 	0 },
	{ "gpioled","sapio", 	0, 18, 			0, 	0 },
	{ NULL, 	NULL, 		0, 0, 			0,  0 }
};


/*
 * Link device names with their drivers.
 */
struct driverinfo config_driverinfo[] = {
/* name, driverp, ninstances (should be -1) */
	{ "root", &root_dr, -1 },
	{ "cpu" , &cpu_dr, -1 },
	{ "saapbus" , &saapbus_dr, -1 },
	{ "sapio", &sapio_dr, -1 },
	{ "gpioled", &gpioled_dr, -1 },
	{ NULL, NULL, 0 }
};


/*
 * Machine early-stage initialization hooks.
 */

void
config_machineinit(void)
{
	/*
	 * Initialize critical devices at startup.
	 */
	__cpu_disable_irq();

	/* disable watchdog */
	*AT91C_WDTC_WDMR = AT91C_WDTC_WDDIS;

	/* set FLASH to high-speed */
	*AT91C_MC_FMR = AT91C_MC_FWS_0FWS;

	/* enable user RESET (magic button on board) */
	*AT91C_RSTC_RMR = AT91C_RSTC_URSTEN | AT91C_RSTC_KEY;

	/*
	 * Initialize oscillators.
	 * Taken from Atmel's examples.
	 */
	/* Set MCK at 48 054 850 */

	/* 1 Enabling the Main Oscillator */
    /* SCK = 1/32768 = 30.51 uSecond
     * Start up time = 8 * 6 / SCK = 56 * 30.51 = 1,46484375 ms
	 */
	*AT91C_PMC_MOR = ( (AT91C_CKGR_OSCOUNT & (0x06 <<8)) | AT91C_CKGR_MOSCEN);

	/* Wait the startup time */
	while(!(*AT91C_PMC_SR & AT91C_PMC_MOSCS))
		;

	/* 2 Checking the Main Oscillator Frequency (Optional) */
	/* TODO */

	/* 3 Setting PLL and divider: */
	/* - div by 14 Fin = 1.3165 =(18,432 / 14)
	 * - Mul 72+1: Fout =   96.1097 =(3,6864 *73)
	 * for 96 MHz the erroe is 0.11%
	 * Field out NOT USED = 0
	 * PLLCOUNT pll startup time estimate at : 0.844 ms
	 * PLLCOUNT 28 = 0.000844 /(1/32768)
	 */
	*AT91C_PMC_PLLR = ( (AT91C_CKGR_DIV & 14 ) 		|
 					(AT91C_CKGR_PLLCOUNT & (28<<8)) |
 					(AT91C_CKGR_MUL & (72<<16)) );

	/* Wait the startup time */
	while(!(*AT91C_PMC_SR & AT91C_PMC_LOCK))
		;
	while(!(*AT91C_PMC_SR & AT91C_PMC_MCKRDY))
		;

	/* 4. Selection of Master Clock and Processor Clock */
	/* select the PLL clock divided by 2: */
	*AT91C_PMC_MCKR = AT91C_PMC_PRES_CLK_2;
	while(!(*AT91C_PMC_SR & AT91C_PMC_MCKRDY))
		;

	*AT91C_PMC_MCKR |= AT91C_PMC_CSS_PLL_CLK;
	while(!(*AT91C_PMC_SR & AT91C_PMC_MCKRDY))
		;

	/* enable clock to all modules */
	*AT91C_PMC_PCER = AT91C_ALL_INT;
	 
	/* initialize USART0 (we clock it in PMC above) */

  *AT91C_PIOA_PDR = AT91C_PA5_RXD0 |        /* Enable RxD0 Pin */
                    AT91C_PA6_TXD0;         /* Enalbe TxD0 Pin */

  *AT91C_US0_MR = AT91C_US_USMODE_NORMAL |  /* Normal Mode */
                  AT91C_US_CLKS_CLOCK    |  /* Clock = MCK */
                  AT91C_US_CHRL_8_BITS   |  /* 8-bit Data  */
                  AT91C_US_PAR_NONE      |  /* No Parity   */
                  AT91C_US_NBSTOP_1_BIT;    /* 1 Stop Bit  */

  *AT91C_US0_BRGR = 48054857 / 16 / 9600;                    /* Baud Rate Divisor */

  /* enable DMA transfers on USART0 */
  *AT91C_US0_PTCR = AT91C_PDC_TXTEN | AT91C_PDC_RXTEN;

  *AT91C_US0_CR = AT91C_US_RXEN  |          /* Receiver Enable     */
                  AT91C_US_TXEN;            /* Transmitter Enable  */

	/* redefine putchar */
	putchar = sausart_early_putchar;
}