File structure grouped by filesystem:

/includes/core/			Core
/includes/api/			API
/includes/acm/			Cache
/includes/auth/			Authentication
/includes/bbcode/		BBCode
/includes/captcha/		Captcha
/includes/db/			DBAL
/includes/search/		Search
/includes/utf/			UTF8-specific files/classes

/includes/classes/		Collection of single classes which we do not want to put into a separate directory. Although later it would be nice to have all of them in one "location".
	acl.php:					ACL/permission class.
	cache.php:					Static class for obtaining cached items/arrays
	session.php:					The session class used for managing sessions.
	template.php, template_compile.php:		The template engine
	user.php:					The user object, handling user-based session and user-specific setups. It defines the users workspace.

/includes/libraries/		Collection of external and "adjusted" libraries we use and do not constitute one "system" in phpBB.
/includes/libraries/diff/	Diff System (Text_Diff-1.1.0 - http://pear.php.net/package/Text_Diff/) - Used By: Updater,
/includes/libraries/sftp/	SFTP (http://phpseclib.sourceforge.net/) - Used By: Transfer Class,


/modules/			Directory holding directories/files for the defined module sections (ucp, mcp, acp, etc.)
/plugins/			Plugins for phpBB (Hooks are now plugins btw... includes/hooks no longer exists)

/develop/			Internal helper files for development. Only present in SVN
/docs/				Documentation, Documents, License file, Coding Guidelines

/cache/				Cache directory for storing files. Needs to be writeable
/store/				Store directory for storing backup files and temporary files. Needs to be writeable
/files/				Files directory for storing attachments and uploaded files. Needs to be writeable