Modules can be stored anywhere, as there is now a set of functions called module_get_filename, and module_set_filename .. which allow system_listing and module_list to specify the locations of the files.
A new function module_load_all() replaces the hardcoded includes in module_init, and loads all modules which have been enabled, using module_load.
module_listing no longer includes files itself, instead it just keeps the listing (and sets the filenames).
This patch is a requirement for the multisite configuration patch, as overriding modules are currently being loaded due to the only protection of loading them is include_once.