Commenting through most of the remaining files.

Fixing logic errors throughout as well

workspace/ts100/src/Main.c

@@ -24,38 +24,39 @@
 int main(void) {
 	RCC_Config(); //setup system clock
 	NVIC_Config(0x4000);
-	Init_Timer2(); //init the timer
+	Init_Timer2(); //init the timers
 	Init_Timer3();
-	GPIO_Config();
-	USB_Port(DISABLE);
-	Delay_Ms(200);
-	USB_Port(ENABLE);
+	GPIO_Config();//setup all the GPIO pins
+
+	USB_Port(DISABLE);//disable the USB hardware
+	Delay_Ms(200);//pause to let hardware stabilize
+	USB_Port(ENABLE);//enable the USB hardware
 	USB_Init();
 	I2C_Configuration(); //init the i2c bus
 
 	Adc_Init(); //init adc and dma
 	if (Get_CtrlStatus() != CONFIG)
-		StartUp_Accelerated();
+		StartUp_Accelerated();//start the accelerometer if not in config mode
 
-	System_Init();
-	Init_Oled();
-	Clear_Screen();
-	Init_Gtime();
-	APP_Init();
+	System_Init();//load known safe values
+	Init_Oled();//init the OLED display
+	Clear_Screen();//clear the display buffer to black
+	Init_Gtime();//init the count down timers
+	APP_Init();//pick operating mode via input voltage
 
-	Disk_BuffInit();
+	Disk_BuffInit();//fill the buffer for the virtual disk
 	Config_Analysis(); //read in config from virtual disk
 	Pid_Init(); //init the pid to starting values
-	Set_gKey(NO_KEY); //reset keys
-	Start_Watchdog(3000);
+	Set_gKey(NO_KEY); //reset keys to all off
+	Start_Watchdog(3000);//start the system watchdog as 3 seconds
 
 	while (1) {
 		Clear_Watchdog(); //reset the Watchdog
 		if (Get_CtrlStatus() != CONFIG && LEAVE_WAIT_TIMER== 0) {
 			Check_Accelerated(); //update readings from the accelerometer
-			LEAVE_WAIT_TIMER = 50;
+			LEAVE_WAIT_TIMER = 50;//reset timer so we dont poll accelerometer for another 500ms
 		}
-		OLed_Display(); //Draw in the Oled display
+		OLed_Display(); //Draw in the Oled display for this mode
 		Status_Tran();  //Handle user input and mode changing
 	}
 }