diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..b7bdf8c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+/Java/MoppyDesk/nbproject/private/
+/Java/MoppyDesk/build/
\ No newline at end of file
diff --git a/Arduino/Moppy.pde b/Arduino/Moppy/Moppy.pde
similarity index 54%
rename from Arduino/Moppy.pde
rename to Arduino/Moppy/Moppy.pde
index d7661aa..79ae5d0 100644
--- a/Arduino/Moppy.pde
+++ b/Arduino/Moppy/Moppy.pde
@@ -1,18 +1,38 @@
 boolean firstRun = true; // Used for one-run-only stuffs;
 
+//First pin being used for floppies, and the last pin.  Used for looping over all pins.
 const byte FIRST_PIN = 2;
 const byte PIN_MAX = 9;
 
+
+/*NOTE: Many of the arrays below contain unused indexes.  This is 
+to prevent the Arduino from having to convert a pin input to an alternate
+array index and save as many cycles as possible.  In other words information 
+for pin 2 will be stored in index 2, and information for pin 4 will be 
+stored in index 4.*/
+
+
+/*An array of maximum track positions for each step-control pin.  Even pins
+are used for control, so only even numbers need a value here.  3.5" Floppies have
+80 tracks, 5.25" have 50 (use 79 and 49).
+*/
 byte MAX_POSITION[] = {
-  0,0,79,0,79,0,79,0,49,0};
+  0,0,79,0,79,0,79,0,79,0};
+  
+//Array to track the current position of each floppy head.  (Only even indexes (i.e. 2,4,6...) are used)
 byte currentPosition[] = {
   0,0,0,0,0,0,0,0,0,0};
+
+//Array to keep track of the direction for each floppy head.  (Only even indexes are used)
 boolean stepDirection[] = {
   false,false,false,false,false,false,false,false,false,false}; // false = forward, true=reverse (i.e. true=HIGH)
+  
+//Current period assigned to each pin.  0 = off.
 unsigned int currentPeriod[] = {
   0,0,0,0,0,0,0,0,0,0 
 };
 
+//Setup pins (Even-odd pairs for step control and direction
 void setup(){
   pinMode(13, OUTPUT);// Pin 13 has an LED connected on most Arduino boards
   pinMode(2, OUTPUT); // Step control 1
@@ -29,15 +49,18 @@ void setup(){
 
 
 void loop(){
+  
+  //The first loop, reset all the drives, and wait 2 seconds...
   if (firstRun)
   {
     firstRun = false;
     resetAll();
     delay(2000);
-    //runOnce();
   }
 
+  //Only read if we have 
   if (Serial.available() > 2){
+    //Watch for special 100-message to reset the drives
     if (Serial.peek() == 100) {
       resetAll();
       Serial.flush();
@@ -50,6 +73,10 @@ void loop(){
   voice();
 }
 
+/*
+The voice() method controls WHEN each pin will be stepped by mod'ing the Arduino system-clock
+against the currentPeriod for each pin.  A period of 0 will skip the pin (i.e. pin is off)
+*/
 void voice()
 {
   if (currentPeriod[2] > 0 && micros()%currentPeriod[2] < 100){
@@ -66,32 +93,45 @@ void voice()
   }
 }
 
-void stepPin(byte pin, byte control_pin, byte wait) {
+/*
+The stepPin() method controls the actual stepping of each pin.  It uses the
+stepDireciton array to determine the state of the direction_pin, and will automatically
+reverse the direction when needed.
+*/
+void stepPin(byte pin, byte direction_pin, byte wait) {
+  
+  //Switch directions if end has been reached
   if (currentPosition[pin] >= MAX_POSITION[pin]) {
     stepDirection[pin] = true;
-  }
-  if (currentPosition[pin] <= 0) {
+  } 
+  else if (currentPosition[pin] <= 0) {
     stepDirection[pin] = false;
   }
+  
+  //Set direction_pin state, and update currentPosition
   if (stepDirection[pin]){
-    digitalWrite(control_pin,HIGH);
+    digitalWrite(direction_pin,HIGH);
     currentPosition[pin]--;
   } 
   else {
-    digitalWrite(control_pin,LOW);
+    digitalWrite(direction_pin,LOW);
     currentPosition[pin]++;
   }
+  
+  //Pulse the control pin
   digitalWrite(pin,HIGH);
   delayMicroseconds(wait);
   digitalWrite(pin,LOW);
 }
 
+//Not used now, but good for debugging...
 void blinkLED(){
   digitalWrite(13, HIGH); // set the LED on
   delay(250);              // wait for a second
   digitalWrite(13, LOW); 
 }
 
+//For a given controller pin, runs the read-head all the way back to 0
 void reset(byte pin)
 {
   digitalWrite(pin+1,HIGH); // Go in reverse
@@ -104,6 +144,7 @@ void reset(byte pin)
   stepDirection[pin] = false; // Ready to go forward.
 }
 
+//Resets all the pins
 void resetAll(){
   for (byte p=FIRST_PIN;p<=PIN_MAX;p+=2){
     reset(p);