Original post here. The tunnel system once ran beneath the entirety of Luceti's main area, namely, the west edge of the barrier to the mountains. Currently the tunnels from the collapsed entrance (the center of the town plaza) to the warehouse at the western end are blocked by John's barrier, and it is there that he conducts his own experiments and removes the Death Penalties. There is no way to access his tunnels.
The eastern tunnels, however, are still accessible, providing a two-day walk beneath the mountains to the desert. Close to the village entrance, there is a side room chosen to contain the laptops that allow for journal entries locked from the Malnosso completely.
Original post here and here. John and Jacob arranged for two laptops (found by the temple ruins) to be offered to the villagers as a method of communicating with their fellows using the journals, but without the Malnosso seeing it. These laptops are used to create secret, village-wide announcements and information entries in the Luceti Locked community; these entries cannot be viewed or hacked by any of the Malnosso. They can be viewed by John since he set up the network, however.