Since 2011 Mars Express has been flying a truly "file-based" concept for commanding the spacecraft and science operations, after a hardware anomaly forced a change from the previous "on-board schedule of commands" approach. As a consequence of the anomaly, new concepts had to be developed and applied to not just the technologies of file transfer and file management, which have received much attention over the years, but also to answer the questions: What are file-based operations? What goes in the files? How are they practically used both on ground and on board? ESA's first generation of deep space missions implement a packet-based large file transfer protocol to enable "files" to be transmitted from ground and guarantee the completeness on-board. However this is a transport-layer protocol and does not address the usage of the files operationally. Similar proposed standards (such as CCSDS File Delivery Protocol) also do not address the functionality of the files, and so by themselves do not necessarily lead to file-based operations. The Mars Express approach relies on seeing spacecraft operations not as a stream of commands, relayed from a mission planning system to the spacecraft via files, but as a collection of discrete activities, with one commanding file per activity. The contents of the file is the responsibility of the science planners, combining elementary sequences as per the rules defined by the spacecraft/payload operations engineers to construct self-contained, fail-safe sets of commands. For example, one science observation activity includes power, thermal, data link and instrument configuration changes that can be combined into one file (of telecommands, as an On-board Control Procedure, or a combination). Rather than individually scheduling the low-level commands, the activity file is simply executed at the correct time. If the observation needs to be modified or cancelled, the file is replaced or deleted. Spacecraft operations can conveniently be abstracted to the simpler paradigm: "which file to execute and when?" -the low-level constraints and resources checking having already been performed at mission planning level when that activity was planned. The ratio of commands-in-files to scheduled "execute" commands (the amount by which operations have been "compressed" by considering the higher-level "activity" file rather than low-level commands) is about 30:1 but is limited by available memory resources. Future missions with larger memories should achieve better than this, with fewer files containing more complex operations, resulting in even more abstracted operations overall. Mars Express has demonstrated a use case and implementation of file-based operations with regards to spacecraft commanding, but this is only half of the picture. The return of science data and housekeeping telemetry remains based on "packet stores". Packet stores are akin to looped SpaceOps Conferences magnetic tapes, in that the data is stored in the order in which it was written. For Mars Express this is not usually a pro...