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The basic configuration of Freenet is done through the configuration menu of the Freenet web interface, fproxy.
Upon starting up your Freenet node for the first time, you will be greeted by a configuration wizard. Your Freenet node will not work until you have completed this wizard. If you are unsure which option is best, leave the default values if applicable, and/or ask for help. All the settings can be changed at a later date if needed.
Freenet nodes connect to each other in 2 different ways: Via the Darknet, where you only connect to trusted friends, and via the Opennet, where you automatically connect to random strangers. The Darknet approach is inherently much more secure than the Opennet because you only exchange traffic with people you trust. You can connect to the Freenet network in both modes simultaneously.
The first-time wizard will either enable or disable Opennet depending on your security levels. Opennet is fully automatic, and will automatically connect to a number of peers suitable for your setup. This, for example, means that the number of Opennet peers will decrease when you add Darknet peers (because Darknet peers are considered more secure), and the number of Opennet peers will increase when you allow Freenet to use more bandwidth.