Another foundation of this process is understanding how systems work. In Flat Galaxy, there are two types of systems: open and closed. The body from the "blocks and boxes" post is an example of a closed system. There are no inputs from outside of the system to inside the system as it has no outside-facing connections. As a result, it is impossible for anything to interact with this system and for the system to interact with anything else. Only the body's component blocks interact with each other, and that's it. Well, that's not very interesting.
To open the system to the world, we must either create a new block with an "external" input (or output) or give one of our existing blocks an "external" input (or output). The system has now gone from closed to open. Much more interesting. Now outside influences can modify the status and behavior of our body system. Of course, the connection into the body will be of a certain type of fuel, but now the possibilities of connections are virtually limitless.
An important note here about "fuel cycle." A fuel cycle is the name I've given to the processing of the effects of input and output. A fuel cycle occurs when fuel leaves or enters a system via an outside-facing input or output. In our closed body system, only one fuel cycle occurs: the initial fuel cycle after the creation of the system*. If the system is still functional after that cycle (i.e. its overall health does not fall below the critical threshold), then it is in a closed equilibrium. Once we open it up, anytime fuel enters the system, we calculate a cycle. This is like the clock cycle in a processor. On the rising clock, we send fuel out of the block into waiting input queues. On the falling clock, we accumulate all existing inputs from input queues into blocks.
There are several important details still to be worked out here, but this is the basic idea.
* This is not a final design decision. I may decide to continually process inputs and outputs in all systems, open or closed and whether or not they have received or lost fuel from an external source.