Restructuring/code clean up

If I created a module and consider it finished (feature wise working order) I start refactoring it, moving code from controller to models to make more sense and document every method.

You can setup your editor to use PHP_CodeSniffer. This could help you to force you to code (php) following a certain style guide. Most editors support this (Sublime, Atom, Php storm) to auto format your code on file save for example or with a shortkey.

You can use PSR-2, the CodeIgniter style guide or your personal preference. The most important thing is readability.

Same applies for html/css, just indent every new element the same way.