Converting an app to CI (conceptualizing the breakdown)

[eluser]CheekyGeek[/eluser]
I'm a newbie to CI, but pretty excited by what I see in the screencast demos and working my way through the User Guide and Upton book.

A couple of questions: Anything glaring "out of date" or deprecated in 1.6.2 from what is in the Upton book? For example, I don't recall the Controller functions in the blog screencast including the

Code:

{parent:: Controller();}

(which Upton says is required, at a minimum, on page 34)

Also, I'd like to convert an existing app to CI, just so I can conceptualize where in the CI folder structure (and MVC concept) the different pieces go. The app uses .php and .phtml pages (where the .phtml mix logic and presentation - an obvious no-no in MVCland).

The app also uses a mixture of PHP and Javascript, for example it uses dynamic dropdown menus values and visible labels from a database table. It populates the dropdown menu on page load if a value has been set and modifies the value if the dropdown has been changed on submit.

It also uses PHP sessions to set a securitylevel parameter that is checked to show/hide (and limit access to) certain functionality. For example, anything under the "admin/" URI will only be loaded if the session securitylevel is set to admin.

The app also does php includes for files like shared/common_lib.php for functions, etc.

I get that any HTML goes in the Views folder, but not sure where the Javascript goes or how I divide up the existing code to fit into the CI folder hierarchy. Anybody have any guidelines to follow - or do you suggest just starting to rewrite the existing apps functionality from scratch the CI way?

TIA for any opinions you might wish to share.