The system directory structure is pretty straightforward:
{$system}/
config/ # mode-specific config files
_mode # The config mode, 'default' by default
_packages # Load these packages in order
default.php # default config overrides
dev.php # shared development server
local.php # local (individual) development server
prod.php # production
stage.php # staging
test.php # testing
include/ # generic include-path directory
package/ # Aura packages
tmp/ # temporary files
vendor/ # Composer vendors
web/ # web server document root
.htaccess # mod_rewrite rules
cache/ # public cached files
favicon.ico # favicon to reduce error_log lines
index.php # bootstrap script
config: The configuration files which are common to all packages.
package: All aura packages like Aura.Autoload, Aura.Di, Aura.Router
etc and the one you are creating will be at packages folder.
tmp: The temporary files, like cached configuration etc
vendor: All the 3rd party libraries, like Doctrine, Propel, Twig
what all you install via composer.
web: The web folder is the one that is exposed to the user.
We will talk more on Package organization and how to create your own package in the next chapter.