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.
Windows
Installer
Installation package needs to follow the rights rules, so it works with UAC. In 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 the
C:\Users\<user>\AppData\Roaming\Factorio
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.
MacOSx
~/Library/Application Support/factorio
Linux
~/.factorio