You have to do it by hand. In Eclipse right click on the project and select add new class and name it after one of your inner classes. Cut and paste the inner class code into the new class window replacing everything that was there.

The only problem is that the new class won't have access to all the P5 code e.g. color(), fill() etc. and it won't have access to private attributes in the main sketch file. The solution to the first is to have an attribute in the new class and in the constructor pass a reference to the Papplet object when you create the object e.g.

1. public class Foo {
2.       privare Papplet app;
3. 
   
4.       public Foo(PApplet app){
5.       this.app = app;
6.       }
7. 
   
8. }

Then in foo you can change P% calls from

noFill();
to
app.noFill();


To create the Foo object in the main sketch it is

Foo f = new Foo(this);


With 15,000 lines of code this is a lot of work that needs to be done one class at a time.