A system and process for improving container flow within a port facility, including improved equipment and software for controlling operation and flow of the equipment in the part facility. The system may include a port facility geographically arranged to separate land operations and water operations. Land operations such as over-the-road missions and rail missions may use landside access areas positioned at one end of a yard including rows of container stacks. Water missions such as loading/discharging a vessel may use waterside access areas positioned at the opposite end of the yard. Automated cranes linked with a terminal operating system may pick/drop/shuffle containers and/or refrigerated containers (“reefers”) within the container stacks. Shuttle trucks may be used to pick/drop containers at quayside access points and the waterside access areas. The shuttle trucks may utilize shared wheelpaths. Software systems may be used to implement various principles of the disclosure.