The application directory stores
- the saves (every save is a zip-file)
- the Mods
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.
Installation by 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.
Installation via Installer
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
Windows Vista and newer (UAC activ):
The application should be by default installed in the Apps. Whereas the data is stored under
Which is equivalent to
Data is stored under