[development] let's cleanup /misc

[Bèr Kessels]

> Got it?  Do it!

Here is a renewed version:
.
|-- README
|-- app
|   |-- modules
|   |   |-- aggregator.modle
|   |   |-- etc
|   |   `-- watchdog.module
|   `-- theme-engines
|        `-- phptemplate
|-- sites
|   |-- default
|   |   |-- modules
|   |   `-- themes
|   |-- site1.com
|   `-- site2.com
|-- database
|   `-- create.mysql etc (also update.inc)
|-- doc
|   `-- INSTALL etc
|-- includes (content similar to now)
|-- public
|   |-- index.php
|   |-- favicon.ico
|   |-- xmlrpc.php
|   |-- images
|   |   `-- druplicon.png
|   |-- index.html
|   |-- javascripts
|   |   |-- controls.js
|   |   |-- dragdrop.js
|   |   |-- effects.js
|   |   `-- prototype.js
|   |-- robots.txt
|   |-- stylesheets
|   |   |-- drupal.css
|   |   `-- module1.css
|   `-- themes
|-- script 
|       |-- install.sh 
|       |-- generate_module.sh 
|       |-- environment_change.sh
|       `-- generate_theme.sh
`-- vendor
    `-- htmlarea

Some notes:

themes, should be under public, they use images, CSS and more.
How supported are symlinks? can we rely on them?  if so, each contrib could be 
symlinked:
/sites/default/modules/mymodule/stylesheets -> /public/stylesheets