Index: git/arch/arm/mach-at91/board-sam9x5cm.c
===================================================================
--- git.orig/arch/arm/mach-at91/board-sam9x5cm.c	2013-04-17 17:15:13.000000000 -0500
+++ git/arch/arm/mach-at91/board-sam9x5cm.c	2013-11-05 17:25:46.511692620 -0600
@@ -18,6 +18,9 @@
 #include <linux/platform_device.h>
 #include <linux/spi/flash.h>
 #include <linux/spi/spi.h>
+#include <linux/spi/eeprom.h>
+#include <linux/i2c/at24.h>
+#include <linux/delay.h>
 #include <linux/fb.h>
 #include <linux/gpio_keys.h>
 #include <linux/input.h>
@@ -103,6 +106,31 @@
 		.irq            = -1,
 	},
 #endif
+	{ /* SPI1_NCS1 to ethernet switch */
+		.modalias = "spidev",
+		.chip_select = 0,
+		.bus_num = 1,
+	},
+	{ /* SPI1_NCS2 to temp sensor */
+		.modalias = "mts-io-board-temp",
+		.chip_select = 1,
+		.bus_num = 1,
+	},
+	{ /* SPI1_NCS3 to daughter card */
+		.modalias = "spidev",
+		.chip_select = 2,
+		.bus_num = 1,
+	},
+	{ /* SPI1_NCS4 to daughter card */
+		.modalias = "spidev",
+		.chip_select = 3,
+		.bus_num = 1,
+	},
+	{ /* SPI1_NCS5 to daughter card */
+		.modalias = "spidev",
+		.chip_select = 4,
+		.bus_num = 1,
+	},
 #endif
 };
 
@@ -111,13 +139,48 @@
  */
 static struct mtd_partition __initdata cm_nand_partition[] = {
 	{
-		.name	= "Partition 1",
+		.name	= "NANDFlash",
+		.offset	= 0,
+		.size	= 256*1024*1024,
+	},
+	{
+		.name	= "AT91Bootstrap",
 		.offset	= 0,
-		.size	= SZ_64M,
+		.size	= 256*1024,
+	},
+	{
+		.name	= "UBoot",
+		.offset	= 256*1024,
+		.size	= 512*1024,
+	},
+	{
+		.name	= "UBoot Config",
+		.offset	= 768*1024,
+		.size	= 640*1024,
 	},
 	{
-		.name	= "Partition 2",
-		.offset	= MTDPART_OFS_NXTBLK,
+		.name	= "UBoot Redundant Config",
+		.offset	= 1408*1024,
+		.size	= 640*1024,
+	},
+	{
+		.name	= "uImage",
+		.offset	= 2*1024*1024,
+		.size	= 6*1024*1024,
+	},
+	{
+		.name	= "Config",
+		.offset	= 8*1024*1024,
+		.size	= 8*1024*1024,
+	},
+	{
+		.name	= "Oem Config",
+		.offset	= 16*1024*1024,
+		.size	= 8*1024*1024,
+	},
+	{
+		.name	= "Rootfs",
+		.offset	= 24*1024*1024,
 		.size	= MTDPART_SIZ_FULL,
 	},
 };
@@ -135,7 +198,8 @@
 	.enable_pin	= AT91_PIN_PD4,
 	.ecc_mode	= NAND_ECC_HW,
 	.has_pmecc	= 1,
-	.pmecc_corr_cap	= 2,
+// MTOCGD3: 4-bit PMECC
+	.pmecc_corr_cap	= 4,
 	.pmecc_sector_size = 512,
 	.pmecc_lookup_table_offset = 0x8000,
 	.partition_info	= nand_partitions,
@@ -170,7 +234,13 @@
 	else
 		cm_nand_smc_config.mode |= AT91_SMC_DBW_8;
 
+	// MTOCGD3 Rev B
+	cm_nand_data.bus_on_d0 = 0;
+	cm_nand_data.rdy_pin = AT91_PIN_PC31;
+
+	// MTOCGD3: disable
 	/* revision of board modify NAND wiring */
+	/*
 	if (cm_is_revA()) {
 		cm_nand_data.bus_on_d0 = 1;
 		cm_nand_data.rdy_pin = AT91_PIN_PD6;
@@ -178,6 +248,7 @@
 		cm_nand_data.bus_on_d0 = 0;
 		cm_nand_data.rdy_pin = AT91_PIN_PD5;
 	}
+	*/
 
 	/* configure chip-select 3 (NAND) */
 	sam9_smc_configure(3, &cm_nand_smc_config);
@@ -189,17 +260,62 @@
  * LEDs
  */
 static struct gpio_led cm_leds[] = {
-	{	/* "left" led, blue, userled1 */
-		.name			= "d1",
-		.gpio			= AT91_PIN_PB18,
+	{	/* default status LED */
+		.name			= "led-a",
+		.gpio			= AT91_PIN_PA24,
+		.active_low		= 1,
 		.default_trigger	= "heartbeat",
 	},
-	{	/* "right" led, red, userled2 */
-		.name			= "d2",
-		.gpio			= AT91_PIN_PD21,
-		.active_low		= 1,
-		.default_trigger	= "mmc0",
+	{
+		.name			= "led-b",
+		.gpio			= AT91_PIN_PA29,
+		.active_low		= 1
+	},
+	{
+		.name			= "led-c",
+		.gpio			= AT91_PIN_PA25,
+		.active_low		= 1
 	},
+	{
+		.name			= "led-d",
+		.gpio			= AT91_PIN_PA26,
+		.active_low		= 1
+	},
+	{
+		.name			= "led-e",
+		.gpio			= AT91_PIN_PA27,
+		.active_low		= 1
+	},
+	{
+		.name			= "led-f",
+		.gpio			= AT91_PIN_PA28,
+		.active_low		= 1
+	},
+};
+
+
+uint8_t mts_id_eeprom[512];
+
+EXPORT_SYMBOL(mts_id_eeprom);
+
+static void mts_id_eeprom_load(struct memory_accessor *macc, void *context)
+{
+	int tmp;
+
+	memset(mts_id_eeprom, 0, sizeof(mts_id_eeprom));
+
+	tmp = macc->read(macc, mts_id_eeprom, 0, sizeof(mts_id_eeprom));
+	if (tmp != sizeof(mts_id_eeprom)) {
+		printk(KERN_ERR "sam9x5: id eeprom read failed: %d\n", tmp);
+	} else {
+		printk(KERN_INFO "sam9x5: read %d bytes from id eeprom\n", tmp);
+	}
+}
+
+static struct at24_platform_data at24c04_data = {
+	.byte_len	= SZ_4K / 8,
+	.page_size	= 16,
+	.setup		= mts_id_eeprom_load,
 };
 
 /*
@@ -207,7 +323,8 @@
  */
 static struct i2c_board_info __initdata cm_i2c_devices[] = {
 	{
-		I2C_BOARD_INFO("24c512", 0x50)
+		I2C_BOARD_INFO("24c04", 0x56),
+		.platform_data = &at24c04_data,
 	},
 };
 
@@ -234,8 +351,12 @@
 	/* LEDs */
 	at91_gpio_leds(cm_leds, ARRAY_SIZE(cm_leds));
 
+	printk(KERN_CRIT "AT91: MTOCGD3 board\n");
+
+	/* MTOCGD3: disable
 	if (cm_is_revA())
 		printk(KERN_CRIT "AT91: CM rev A\n");
 	else
 		printk(KERN_CRIT "AT91: CM rev B and higher\n");
+	*/
 }
Index: git/arch/arm/mach-at91/board-sam9x5ek.c
===================================================================
--- git.orig/arch/arm/mach-at91/board-sam9x5ek.c	2013-04-17 17:15:13.000000000 -0500
+++ git/arch/arm/mach-at91/board-sam9x5ek.c	2013-11-01 12:16:09.080917828 -0500
@@ -23,6 +23,7 @@
 #include <linux/leds.h>
 #include <linux/clk.h>
 #include <linux/delay.h>
+#include <linux/wl12xx.h>
 #include <mach/cpu.h>
 
 #include <video/atmel_lcdfb.h>
@@ -53,12 +54,10 @@
 	/* Initialize processor and DBGU */
 	cm_map_io();
 
-	/* USART0 on ttyS1. (Rx, Tx) */
-	at91_register_uart(AT91SAM9X5_ID_USART0, 1, 0);
-	/* USART1 on ttyS2. (Rx, Tx) */
-	at91_register_uart(AT91SAM9X5_ID_USART1, 2, 0);
-	/* USART2 on ttyS3. (Rx, Tx) */
-	at91_register_uart(AT91SAM9X5_ID_USART2, 3, 0);
+	// MTOCGD3: GPS on UART0 as ttyS1 with Rx/Tx only
+	at91_register_uart(AT91SAM9X5_ID_UART0, 1, 0);
+	// MTOCGD3 Rev A: Daughter card serial on USART1 as ttyS2 with RTS/CTS
+	at91_register_uart(AT91SAM9X5_ID_USART1, 2, ATMEL_UART_CTS | ATMEL_UART_RTS);
 }
 
 /*
@@ -89,34 +88,65 @@
  * MACB Ethernet devices
  */
 static struct at91_eth_data __initdata ek_macb0_data = {
-	.is_rmii	= 1,
+	.is_rmii	= 0,
+	.phy_irq_pin	= 0,
 };
 
+/* MTOCGD3: no macb1
 static struct at91_eth_data __initdata ek_macb1_data = {
 	.phy_irq_pin	= AT91_PIN_PC26,
 	.is_rmii	= 1,
 };
+*/
 
 
 /*
  * MCI (SD/MMC)
  */
-/* mci0 detect_pin is revision dependent */
+// MTOCGD3: MCI0 is BT/Wifi
 static struct mci_platform_data __initdata mci0_data = {
 	.slot[0] = {
 		.bus_width	= 4,
+		.detect_pin	= -1,
 		.wp_pin		= -1,
 	},
 };
 
+// MTOCGD3: MCI1 is SD card slot
 static struct mci_platform_data __initdata mci1_data = {
 	.slot[0] = {
 		.bus_width	= 4,
-		.detect_pin	= AT91_PIN_PD14,
-		.wp_pin		= -1,
+		.detect_pin	= AT91_PIN_PA1,
+		.wp_pin		= AT91_PIN_PA0,
 	},
 };
 
+// MTR: Wi-fi
+static void wl12xx_enable(int poweron)
+{
+	if (poweron) {
+		at91_set_gpio_output_with_pullup(AT91_PIN_PC1, 0, 0);
+		msleep(10);
+		at91_set_gpio_output_with_pullup(AT91_PIN_PC1, 1, 0);
+		msleep(100);
+		printk(KERN_INFO "sam9x5: WLAN Enabled\n");
+	}
+	else {
+		at91_set_gpio_output_with_pullup(AT91_PIN_PC1, 0, 0);
+		msleep(10);
+		printk(KERN_INFO "sam9x5: WLAN Disabled\n");
+	}
+};
+
+// MTR: Wi-fi
+struct wl12xx_platform_data mtr_wlan_data  __initdata = {
+	.irq = AT91_PIN_PC2,
+	/* ref clock is 38.4 MHz */
+	.board_ref_clock = WL12XX_REFCLOCK_38,
+	/* toggles the WLAN_ENABLE pin */
+	.set_power = wl12xx_enable,
+};
+
 /*
  *  ISI
  */
@@ -330,9 +360,11 @@
  * I2C Devices
  */
 static struct i2c_board_info __initdata ek_i2c_devices[] = {
+#if 0
 	{
 		I2C_BOARD_INFO("wm8731", 0x1a)
 	},
+#endif
 #if defined(CONFIG_KEYBOARD_QT1070)
 	{
 		I2C_BOARD_INFO("qt1070", 0x1b),
@@ -388,18 +420,24 @@
 	bool config_isi_enabled = false;
 
 	cm_board_init(&cm_config);
-	ek_board_configure_pins();
+	// MTOCGD3: disable
+	//ek_board_configure_pins();
 	/* Serial */
 	at91_add_device_serial();
 	/* USB HS Host */
 	at91_add_device_usbh_ohci(&ek_usbh_fs_data);
 	at91_add_device_usbh_ehci(&ek_usbh_hs_data);
 	/* USB HS Device */
+	// MTOCGD3: set usb device vcc pin
+	ek_usba_udc_data.vbus_pin = AT91_PIN_PC7;
 	at91_add_device_usba(&ek_usba_udc_data);
 	/* Ethernet */
 	at91_add_device_eth(0, &ek_macb0_data);
+	/* MTOCGD3: no macb1
 	at91_add_device_eth(1, &ek_macb1_data);
+	*/
 	/* MMC0 */
+	// MTOCGD3: MCI0 for BT/Wifi
 	at91_add_device_mci(0, &mci0_data);
 	/* I2C */
 	if (cm_config & CM_CONFIG_I2C0_ENABLE)
@@ -409,6 +447,15 @@
 		at91_add_device_i2c(0,
 				ek_i2c_devices, ARRAY_SIZE(ek_i2c_devices));
 
+	// MTOCGD3: Wi-fi
+	at91_set_gpio_input(mtr_wlan_data.irq, 0);
+	at91_set_deglitch(mtr_wlan_data.irq, 1);
+
+	if (wl12xx_set_platform_data(&mtr_wlan_data))
+		pr_err("error setting wl12xx data\n");
+
+/* MTOCGD3: no LCD */
+#if 0
 	if (cpu_is_at91sam9g25()) {
 		/* ISI */
 		/* NOTE: PCK0 provides ISI_MCK to the ISI module.
@@ -434,13 +481,10 @@
 		/* Touch Screen */
 		at91_add_device_tsadcc(&ek_tsadcc_data);
 	}
+#endif
 
-	/* MMC1 */
-	/* Conflict between SPI0, MCI1 and ISI pins.
-	 * add MCI1 only if SPI0 and ISI are both disabled.
-	 */
-	if (!(cm_config & CM_CONFIG_SPI0_ENABLE) && !config_isi_enabled)
-		at91_add_device_mci(1, &mci1_data);
+	// MTOCGD3: MCI1 to SD Card
+	at91_add_device_mci(1, &mci1_data);
 
 #if 0
 	if (cpu_is_at91sam9x25() || cpu_is_at91sam9x35())
@@ -452,6 +496,8 @@
 		at91_add_device_can(0, NULL);
 #endif
 
+/* MTOCGD3: disable things we don't have */
+#if 0
 	if (cpu_is_at91sam9x25() || cpu_is_at91sam9x35())
 		/* this conflicts with usart.1 */
 		at91_add_device_can(1, NULL);
@@ -478,6 +524,9 @@
 	else if (config_isi_enabled)
 		printk(KERN_CRIT
 			"AT91: ISI conficts with MCI1, disable MCI1\n");
+#endif
+
+	printk(KERN_CRIT "AT91: MTOCGD3 board EK init\n");
 }
 
 MACHINE_START(AT91SAM9X5EK, "Atmel AT91SAM9X5-EK")
Index: git/arch/arm/mach-at91/at91sam9x5_devices.c
===================================================================
--- git.orig/arch/arm/mach-at91/at91sam9x5_devices.c	2013-04-17 17:15:13.000000000 -0500
+++ git/arch/arm/mach-at91/at91sam9x5_devices.c	2013-11-01 12:16:09.080917828 -0500
@@ -543,11 +543,11 @@
 #endif
 
 	/* input/irq */
-	if (data->slot[0].detect_pin) {
+	if (data->slot[0].detect_pin > 0) {
 		at91_set_gpio_input(data->slot[0].detect_pin, 1);
 		at91_set_deglitch(data->slot[0].detect_pin, 1);
 	}
-	if (data->slot[0].wp_pin)
+	if (data->slot[0].wp_pin > 0)
 		at91_set_gpio_input(data->slot[0].wp_pin, 1);
 
 	if (mmc_id == 0) {		/* MCI0 */
@@ -849,7 +849,8 @@
 	.num_resources	= ARRAY_SIZE(spi1_resources),
 };
 
-static const unsigned spi1_standard_cs[4] = { AT91_PIN_PA8, AT91_PIN_PA0, AT91_PIN_PA31, AT91_PIN_PA30 };
+// MTOCGD3: SPI1 chip selects on pins SPI1_NCS1 to SPI1_NCS5
+static const unsigned spi1_standard_cs[5] = { AT91_PIN_PC15, AT91_PIN_PC16, AT91_PIN_PC17, AT91_PIN_PC18, AT91_PIN_PC19 };
 
 void __init at91_add_device_spi(struct spi_board_info *devices, int nr_devices)
 {