Structure of Web Development files, when using Version Control

I am planning on using Version Control (Mercurial) for my web applications. I am going to try it out first on my laptop. I would think now that I should restructure my folders to get them all in the same respository.

I am using a PHP framework (Kohana 3) so my folder structure is as follows at the moment.

kohana
    + application
    + modules
    + system
htdocs
    + css
    + images
    + js
    index

I'm not really sure of the best way to make this work, but I was thinking it would be good if I could reference all my files in the same repository (css, js, and php). How should I structure my files开发者_开发知识库 to do that? And what is this trunk, tag, branch stuff I see when I look at other possible structures online?

Thanks.

Look here for explaination of tag, trunk, branch