Heehee! Like jimjam said, we'll compile a list soon. As soon as my current run dies I'm going to start doing runs dedicated to information gathering. I'll be taking screenshots of mob stats, running commands just for the hell of it, etc. You'll hear from us soon enough 
From Reddit
/r/CogmindFabricator
Build
Builds the loaded schematic. Will not work if nothing is loaded.
Load(PARTNAME)
This command is used to load a schematic that you know into the machine. Unfortunately, it does not work on schematics you haven't downloaded
Recycling Unit
Recycle(PARTNAME)
Recycles a part from your inventory into matter. Be wary of the fact that the collected matter is taken into the machine!
Report(Matter)
Outputs the amount of matter currently in the machine.
Retrieve(Matter)
Outputs the matter currently in the machine.
Repair Station
Refit
If you have below X number of slots filled, fills those slots with backup cores, hover pads, and lasers. On one of the later levels I think I got three cores and hover pads, so the amount is variable based on depth, probably.
Repair
Repairs a scanned part. Takes time to complete. Don't just start a repair and run away without your part! I did... If this step fails, your part might be damaged beyond use, so use responsibly.
Scan(PARTNAME)
Scans a part from your inventory into the machine so it can be repaired.
Scanalyzer
Insert(PARTNAME)
Loads a part from your inventory into the machine so it can be scanned.
Scanalyze
Downloads a schematic to your memory based on the part. Schematics are used with matter at a Fabricator to build copies. This step can damage your part beyond use, so use responsibly.
Terminal
Ah, the main course. Here we get into the meaty stuff. This is the section I need the most help on.
Access(Branch)
This command will give you the locations of any Branch stairwells. Because we are in Alpha 1, most of the Branch stairs don't work, so this command is not useful (yet).
Access(Emergency)
This command will scan a small radius around you and highlight any 'emergency' doorways, a.k.a. hidden doors. I don't mean to start making judgement calls, but it's not very useful because the sweep radius is too small - something like 25~40 blocks.
Access(Main)
My personal favorite, this one will download the locations of all main stairways on the current floor. Very difficult hack but cathartic when it succeeds.
Alert(Check)
Outputs the current security level of the floor. Use to quantify how much trouble you've been up to.
Alert(Purge)
Lowers the current security level of the floor, presumably one step at a time.
Analysis(BOTNAME)
Gives a little bio on a unit. BOTNAME must be exact, e.g. 'Analysis(M-28 Smith)'. You cannot just type in Mechanic.
Control(Machines)
Attempts to sabotage a machine elsewhere on the map, i.e. a fusion reactor. If successful the machine detonates, drawing attention (perhaps away from you). Can also be used multiple times AFAIK.
Enumerate(Assaults)
Enumerate(Exterminations)
Enumerate(Maintenance)
Enumerate(Squads)
Enumerate(Transport)
This one has many possible states. It will give you the current location of the targets. 'Assaults', 'Exterminations', and 'Squads' are all combat unit-related. 'Maintenance' will give you the location of Mechanics. 'Transport' will tell you where the haulers are ('a' and 'A'). How useful this information is is variable.
Index(Fabricators)
Index(Repair Units)
Index(Terminals)
Index(Scanalyzers)
Index(Recycling Units)
Use this to gain the locations of all requested devices. There is a discrepancy between what we know as 'Repair Stations' being called 'Repair Units' on the command, and same with 'Recycling Units'.
Index(Machines)
Downloads coordinate data for ALL machines on the current floor.
Inventory(Components)
Lists stockpiles and their locations. They get marked on your radar.
Inventory(Prototypes)
Lists prototypes and their locations. These get marked on your radar.
Manifests
Displays data on what haulers are hauling. Will NOT give you the locations on the haulers.
Prototypes
Downloads data on prototypes. I have not lived to test this, but presumably when you come across the pile of them you will be able to tell what they are at a glance (i.e. 'Imp. EM Shotgun', not 'Prototype Energy Weapon'). Of note: this command only gives you info on a few prototypes. It must be used multiple times if you want comprehensive information.
Query(NAME)
Downloads a text article on your subject. Viewed on Terminals as "Record [Earth]" and such. Presumably this command can be used in innumerable ways - Kryzati seems to have created quite the lorebook. My interest is piqued!
Recall(Assault)
Recall(Extermination)
Recalls the given squad. Heck, there's probably a 'Recall(Squad)' command too, but until I verify it I'm not listing it. What does recall mean, anyways? Do they disappear off the map instantly? I once saw a C-30 Carrier go up the stairs. 2SPOOKY
Schematic(NAME)
The golden goose. Use this command to attempt to download the target schematic. This can be used even on parts you haven't seen - I once downloaded 'Biomechanical Wings' on floor -8, even though that's an item I discovered on -3. It gets better: use this to download schematics on bots too. Again, you have to know the exact name (e.g. 'P-80 Sage'), but that's a given at this point. Someone try to fab me a 'B-99 Colossus' and let me know how that goes. Basically, if you've seen a screenshot of it, you can download it (subject to the usual whims of hacking, of course).
Congratulations! You are now computer-literate. I repeat, if you have any additional information, please drop a comment either here or on the Grid Sage Forums and I will update this ASAP. I might have made a mistake somewhere, or there may be other hidden uses to commands.
