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
C:\Program Files\Factorio
MacOSx
~/Library/Application Support/factorio
Linux
~/.factorio