I have a program that reads XML data which is gathered and updated daily using a cronjob on my server. The problem is that when Processing  exports a Java applet it seems to embed the XML data into the code instead of keeping it independent. How can I have it function as an applet on the web but still read from XML stored on my server

My program is here: http://zakgreene.com/deep

Great! Thanks!

I've run into another somewhat related bug I wonder if you could help with.

I'm trying now to delve into objects, which I was previously unfamiliar with, but I think it will help my program and make it easier to add and expand. I'd been using this basic syntax in setup() to read my XML files:

Code:

xml = new XMLElement(this, "state1.xml"); 

Yet now I'm trying to do that within an object called Shape. So I'm getting an error because "this" now referes to the object Shape. This is probably a no-brainer but I can't for the life of me figure it out. How do I refer to the parent object, or in this case, the sketch itself. I can't find an example of anything other than "this" as the first argument to XMLElement().

this refers to the current object, so if you are in a Shape class, it refers to the current instance of Shape, as you found out.
Libraries show to pass this as parameter outside of classes, so it refers to the current PApplet instance, automatically created by Processing.
The classical way to handle the problem is to do like libraries, and make the constructor of your class to accept a PApplet parameter:
Code:

// Object creation in the sketch:
Shape sh = new Shape(this, "state1.xml");

// Constructor of the class:
public Shape(PApplet pa, String fileName) // Others params possible, of course
{
  xml = new XMLElement(pa, fileName); 
  // Etc.
} 

Perfect! Thank you!