<php require('file.html')>

require

<php require('file.html')>

I'm looking for a system that generates HTML templates from
HTML with includes.

I'm looking for a way to use includes while still able to send
a HTML/CSS/JS package off to a client that can be opened
through clicking .html files.

The system doesn't have to be PHP based, it can be a shell
script thats loops through files ("generate html") or
something else.

I'm looking for something as simple as possible that doesn't
force me into a directory structure (one level of templates,
just /css /images/ folders)

using apache ant you can "generate" a list to include in your project,
but if you want the real deal; get your hands dirty on backbone.js, it uses the insanely handy underscore template engine,
other html/js template engines include handlebars.js or moustache.js

This might not be the exact thing you're looking for, but it's close.

http://middlemanapp.com/
http://middlemanapp.com/templates/templates-layouts-partials/