Restructuring/code clean up

OK so you got some code and it works pretty nicely except, it is all sort of over the place and not really organised.

You want to structure it in a way that is organised because it is something everyone has the potential to see and use and possibly amend.

This includes a logical and sensible file structure, organised logical string of methods, and tidy html views and css js files.

Where do you start?

I looked at using html/css beautifiers to dump out better view files. Tried to keep consistent naming of methods and spacing, might use a PHP beautifier on it too. File structure is pretty much own preference at the minute.

What do you do, this question is specifically aimed at github users who have clean readable code.

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