Application directory
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The application directory stores
- the saves (every save is a zip-file)
- the Mods
- scenarios
- configuration.
The directory structure is self-explaining.
You can delete for example the configuration-file, it will be generated new with the defaults. It is recommended to create backups from this directory, before you install a new version.
Zip-package
Zip package is just one Factorio directory that doesn't need to be installed, all the saves are there locally easy to find.
Installer
Windows
Installation package follows UAC. For that case the factorio directory is where you install it (Program files by default) and the user data (saves, player data etc) are stored in
C:\Users\<username>\AppData\Roaming\Factorio
Windows Vista and newer (UAC activ):
%appdata%\factorio
MacOSx
~/Library/Application Support/factorio
Which is equivalent to
/users/<username>/Library/Application Support/factorio
Linux
~/.factorio