CSS: I only use one stylesheet. I just keep appending to the bottom as I go along. I usually place a comment before each page-specific set of rules. Ctrl+F if I need to edit something.
Javascript: Usually include only one library, and maybe a few plugins. Used to throw any page-specific JS directly into the header of that page, but I find it a bit ugly and mixes 'behaviour' with data. So I'm starting a new paradigm --
MVCB -- Model, View, Controller, Behaviour. MVC is great for desktop apps with rather static UIs, but when you add lots of JS I think it calls for an extra layer of abstraction.
Thus, my original file structure:
index.php
app
config
bootstrap.php -- code that needs to run before anything else, or functions that don't really fit elsewhere
core.php -- timezone, database, and misc settings
routes.php -- default routes
layouts -- layout/template files
flash -- layouts for one-time popup messages
objects -- all files are stored in the same folder as the controller to keep directories
smaller and ease reusability
object
controller.php
model.php
routes.php -- object-specific routes to override default routes
behaviours -- page-specific javascript files
action.js -- included automatically on that page if this file exists
views
action.php -- the view for this action
public -- static media files, sometimes called "assets"
favicon.ico
xrds.xml
css
img
js
uploads
core
app.php -- initializes stuff
controller.php -- default controller
dispatcher.php -- includes everything and calls all the appropriate functions
model.php -- default model that all other models inherit from
components -- helper functions to used in controllers
datasources -- mysql, oracle, flat-file...
helpers -- functions to be used in views and layouts
structures -- model helpers such as tree or polymorphic behaviours
utils -- functions that are useful everywhere
libs -- 3rd party libs
.htaccess
Options -Indexes
RewriteEngine On
RewriteCond %{REQUEST_URI} !^/app/public/
RewriteCond %{DOCUMENT_ROOT}/app/public%{REQUEST_URI} -f
RewriteRule .* /app/public/$0 [L]
RewriteCond %{REQUEST_URI} !^/app/objects/
RewriteRule ^([^/]+)/(.+\.js)$ /app/objects/$1/behaviours/$2 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule .* /index.php?url=$0 [L,QSA]
