Is there anywhere a good writeup on Drupal directory structure?
I haven't seen one, so let's start a list right here. In Drupal 5, 6 and 7 the structure looks like this:


includes - include files with php functions and classes that make up the Drupal API
misc - miscellaneous assets like javascript files and images
modules - Drupal core modules (not meant for contrib and custom modules)
profiles - installation profiles
scripts - shell scripts for developers and administrators
sites - all files that are added by a developer to create a site


sites/all/libraries - 3rd party libraries, eg. a wysiwyg editor
sites/all/modules - contributed and custom modules
sites/all/themes - contributed and custom (sub)themes
sites/default - contains the default settings.php
sites/default/files - the default directory for user-uploaded files
sites/example.com/modules - the site-specific modules directory in a multisite structure
sites/example.com/themes - the site-specific themes directory in a multisite structure
sites/example.com/files - the site-specific directory for user-uploaded files in a multisite structure

themes - Drupal core themes