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 project. Some things the nanites cannot build on the fly, and must be constructed beforehand. 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 crafter 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 modifier the agent knows, but cannot directly give commands to nanites. After receiving the request, the bubble server automatically deducts 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 has to do is apply the nanites to the collected parts, and stand back. The nanites rearrange the objects around, part by atomic part, until 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 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 commands at once, and send them over as needed to maintain the builder nanites' functions, this reduces the load on the main server, thus creating an environment more suitable for the nanites to do their job.
A special note
Because of the manor in which crafting operates, the final product should pay respect to the recipe and modifiers that were used to make it. This is not to say a 100% match between the final concept of the item and what recipe and modifiers you used is suggested, but, it would be more appropriate to use a laser or beam schematic if you are making some kind of laser or beam weapon, and it would be a better match if you used a melee schematic for making an axe, sword, dagger, etc. Theme pays respect to mechanics and mechanics follow theme.