At this point, you will probably want to open and edit a module's source code. To open the source file of a module, you could use the Open File item in the file menu, but I strongly suggest that you don't. If you know the name of the module whose source you want to edit, you should instead press ctrl-o, which will spawn a popup which looks like this:
Now, type in the name of the module (and only the name--the full package path is optional and can be used to resolve ambiguities between identically named modules in different packages) and press enter. That was much more efficient than searching through a tree view of your project, wasn't it?
Navigating a Single File
Don't worry. The bodies of your functions have not been removed—they've just been folded out of view. There are two ways to unfold them: by clicking on the corresponding + icon in the left margin or by moving the caret to the corresponding line and pressing ctrl-'.
The reason Game Kitchen hides your function bodies is to give you a high level view of a file before you delve into the details.
If you want to view two modules side-by-side, ctrl-/ will move the current source file into the other tab.
Creating a New Module
To create a new module, press ctrl-n. The Create Module dialog will appear on your screen. In the drop-down box to the left of the Okay and Cancel buttons, choose Basic Class System--this is the default class system which installs with Game Kitchen. Type the name of the module you want to create ("player" for example) into the Class Path field and press enter. A new tab will be created containing template source code for a new class defined using Basic Class Sytem.
Note that Class Path should contain a module name and not a file name. Do not append ".lua" to the end of it.