How Crafting Works
What are Builder Nanites, Recipes, and Modifiers?
Builder nanites are blank industrial nanites that are able to accept commands that do not directly involve things like infection and mutation. Lower grade, they are perfect for a simple, one use, task like construction. Stored in glass vials, these nanites simply await commands to be executed. A recipe is a set of instructions for the nanites to follow to construct a particular object. It is all simply commands to be executed by various batches of builder nanites upon objects provided by the crafter to make a functioning finished projects. Some things the nanites cannot build on the fly, and must have constructed before hand, however most of these already have Recipes for them (See Battery and Nanite Power Brick), or otherwise available (See Mako Shark). A modifier is exactly that, a program meant to modify one of the recipe programs. The craft must have a general idea about what they are building to know how much salvage to use, which modifiers are compatible, and how to make sure the end product works as designed and intended. This is the reason for crafting skill levels.
How this process works
To begin with, the one doing the crafting assembles the necessary parts. Salvage, pre-built gear, and builder nanites collected, the agent then sends to the nearest bubble server a request for nanite instructions for the recipe data stored in their comm. The comm can store the basics of each recipe and recipe modifier the agent knows, but cannot directly give commands to nanites. After receiving the request, the bubble server automatically deduces the cost of this service from the comm of the requester, and transmits, bit by bit, the requested data to the builder nanites indicated by the agent's comm. That done, all the agent then has to do is apply the nanites to the collected parts, and stand back! The nanites rearrange the objects around, part by atomic part, til it is what the recipe and modifiers say it should be.
About Craft rooms
The main bubble server is usually very busy running a lot of different tasks needed by the bubble itself, and taking CPU time away from it is both costly and inefficient. In each of the craft rooms is a much smaller server, useful really, only for storing and relaying very specific and less complex code, perfect for storing and relaying the commands of a recipe and its modifiers. By being able to take all the command at once, and send them over as needed to maintain the builder nanites' functions, this reduces the load on the main server, and creates an environment more suitable for the nanites to do their job.