Walkthrough for The Cake Factory

Act I: The Cake Factory offices

LOBBY, FLOOR 1
Items: screwdriver, "Façade" magazine, vent, and (maybe) Comfortable couch
Puzzle: Combine items.

Puzzle explanation: Combine items.
As instructed by Xanadu, you're expected to use the screwdriver (ac---) with the vent (--0Au) to continue on into the air ducts (giveaway code ac0Au).

AIR DUCTS, BETWEEN FLOORS
Destinations: Restroom.

RESTROOM, FLOOR 2
Items: thief/supply puzzle items
Puzzle: Access to IT
Destinations: Break room, Meeting room

Puzzle explanation: Access to IT
You aren't necessarily expected to visit IT yet, but you can (and will have to) through this puzzle.
This puzzle has many clues, and can be very simple, but perhaps because the link is actually five links, may not be immediately obvious. In short: from the five links, build the link to the next giveaway backwards. Clues:
"Tit'n em? Trap Ed, Mo, or "S.S. Ape" (Doc)!", without punctuation, is "Code Pass Room Department IT" backwards, or "IT Department Room Pass Code" backwards again.
The giveaway game is "Mirror's Edge".
When looking at the mirror, you notice the toilet stall walls, where this message is scrawled.
The links in the message are all linked to "IT/--x--", letting you know that decoding it will give you access to the IT department.
(Customer Service) The sign near the keypad: "See 'Yourself' for the IT Department Room Pass Code" vaguely hints at using a mirror, and additionally gives the exact "IT Department Room Pass Code" phrasing used in the backwards message.
(Customer Service) CS Rep #15 gives the clue to use "door number 2", a rather juvenile clue to use the restroom, and I probably should have italicized only "number 2" instead of also italicizing "door".
(Customer Service) CS Rep #26 suggests that you should "drink a lot of water, get all cross-eyed, and get the code [for IT]" (go to the bathroom, and read the text backwards, was this hint's intention).
(Customer Service) The 'Door across the east hall to IT' lets you know you should be looking in the restroom for access to IT.
(Orders & Fulfillment) The interrogation of Gamecreature only divulged a need to use the bathroom.
(Orders & Fulfillment) Fulfillment Processor #11 suggests that graffiti is a major clue to get into the IT department.

MEETING ROOM, FLOOR 2
Items: thief/supply puzzle items

BREAK ROOM, FLOOR 2
Items: thief/supply puzzle items
Destinations: Customer Service, Orders & Fulfillment

CUSTOMER SERVICE, FLOOR 2
Items: thief/supply puzzle items
Destinations: HR

ORDERS & FULFILLMENT, FLOOR 2
Items: thief/supply puzzle items

HUMAN RESOURCES, FLOOR 2
Items: thief/supply puzzle items
Puzzle: Catch the thief!

Puzzle explanation: Catch the thief!
This is the big one, and although it doesn't technically require you to have accessed the IT Department, you'll need to later anyway. The rooms involved in this puzzle include: IT, HR, Customer Service, Orders & Fulfillment, Break Room, Meeting Room, and Restroom.
If you've been keeping good notes as you pass through each room, this isn't terribly hard, just very very tedious. (Something I'm normally against in adventure games, but launching the Cake Factory in time for my Cake Day meant the puzzle had to stay.)
HR needs you to find whoever has an item that doesn't belong to them, and to return it to the victim. "Thief, item, victim, got that? Thief + item + victim."
The best way to solve this puzzle is a combination of the ItsTooHard puzzles that were provided after this puzzle was proving too difficult (I would have put all 60 questions on one page, but there's a 25(?) question limit)...
(Also, the order of the items on the ItsTooHard wasn't entirely random: it's alphabetical by their "?=X" value -- not that that really helps.
But the ITH isn't really necessary to solve the puzzle; it just makes sure you have every item accounted for until there are two people, and one item, left.)
...and the intended solution: use the "Anonymized Employee Profiles, Floor 2" data from HR. Every one of the "Job performance notes" matches one of the suspects. The "Item code" gives a hint as to what item the person possesses. The color "Remark" matches the color of their item, in the case of items with the same "Item code", such as the various-coloured "H2G2" Hitchhiker's Guide to the Galaxy books.
From this information, the commentary from each of the employees, and contextual clues within the narrative (e.g. "briny green slime" is from the "Pickle Rick" toy), you can eventually deduce who the thief is, as well as their victim.
A few of the item codes were admittedly vague in context. GLotHotGF is "Glorfindel, Lord of the House of the Golden Flower", and JAPvdL is "Julian Alfred Pankratz, viscount de Lettenhove" (aka Dandelion). The abbreviations for these were spelled out in words in the ItsTooHard puzzle, at least.
Additionally, the Nebuchadnezzar model is also counted as a video collection, as mentioned in the text, query string ("?video-AND-model=t"), and ItsTooHard puzzle, but this was really the result of that particular item being a perfect match for "gray" and "The Matrix" rather than being an intentional twist in the puzzle. (Many, if not most, of the items assigned to people can be found in real life.)
If you have a question about how to assign ownership for a specific item, please let me know!
Eventually, you will settle on two people who both have an interest in Australia.
One person has a notebook from the Daintree Eco Lodge, found in Australia (personal note: that lodge looks amazing!), and the other has no item, but mentions having visited Australia.
The code for the next location after discovering the thief, the stolen item, and the victim, and putting the three pieces together, is Rn8wq, and that leads you to the supply window.

But first! You should go visit the IT department, if you've somehow skipped over it so far, to make sure you have the last few items.

SERVER ROOM / IT DEPARTMENT, FLOOR 2
Items: thief/supply puzzle items
Puzzle: IT equipment order, The perfect IT cake
Both puzzles are assigned here, but solved elsewhere.

SUPPLIES & REQUISITIONS WINDOW (from Human Resources), FLOOR 2
Puzzle: Supply inventory

Puzzle explanation: Supply inventory
This... is the other big one. But if you've held onto your notes, or just realize that you can use the ItsTooHard puzzle (which explicity states the item type for every item apart from the stolen item), this can be fairly easy.
Catalog every one of the 61 items (62 if you count the Nebuchadnezzar twice) into their category, and total up the cost.
You should have...
1 Instruments
6 Illustrations, Prints, and Paintings
7 Single or Multi-Video Collections, Music Albums
13 Figurines, Statuettes, Models, and Desk Toys
12 Clothing (Hats, Shirts, Jerseys)
11 Posters, Photos, and Postcards
11 Books, and Notebooks
1 Lunchboxes, Bottles, Mugs
Which should total up to $10,678.
Translating that value using the "Accounting cost code translation table (duplicate copy)" will give you access to Accounting.

Accounting (forgot to capitalize and add "Floor 2", an oversight on my part...)
Items: microscopic black hole, (optional) Door to Management
Puzzle: IT equipment order

Puzzle explanation: IT equipment order
Over in the IT department, they gave you a list of items to check out from the Supply department.
From the Supply department, you have to match those items to a "Supply code".
Finally, in Accounting, you match the Supply codes with a cost, add them up, and use the same "Accounting Cost Code translation table" as you used for the Supply inventory puzzle to access the next room.
(The 3D printer is the only item you can't match to a supply code until you visit Accounting.)
You should have...
3x 1yr puffin cloud extension
1x zombiesoft business apps renewal (pro edition)
6x Smellybook Pros (orange)
4x SEVEN tablets
1x ZeeZaw XY26 LB
7x UPS
24x 3TB P HDDs
1x 3D printer (least expensive)
4x Bigfoot-12 Desktops
1x NomsNTea Large
...which results in a total of $24,359.
And that leads you to the Design department.

THE DESIGN TEAM'S OFFICES, FLOOR 2
Items: (optional) Door to Management
Destinations: Packaging (downstairs)

With most of the heavy lifting out of the way, the path is clear to Act II! (Act II is much easier...)

Act II: The Cake Factory tour!

PACKAGING, FLOOR 1
Items: miscellaneous, intended to be used in a junkpile, but I never found the time to really add to it (same goes for subsequent rooms in the Cake Factory).
Destinations: Quality Control

QUALITY CONTROL, FLOOR 1
Items: postcard
Puzzle: postcard

"Puzzle" explanation: The postcard code leads to the Decorating area.

DECORATING, FLOOR 1
Items: a swirling set of characters (NWNWSWS) (these might be easy to miss, as they are not linked with a query string like most items)
Destinations: Cooling racks

COOLING RACKS, FLOOR 1
Items: Svalinn heat shield
Destinations: Ovens

OVENS, FLOOR 1
Items: solar oven
Destinations: Mixers

MIXERS, FLOOR 1
Items: Járngreipr dough hook gauntlet
Destinations: Vats and hoppers

Vats and Hoppers, FLOOR 1 (missed capitalization again... whoops!)
Items: Lúin "Fireball" thermal lance, the code
Puzzle: fridge door

"Puzzle" explanation: Use the code to open the fridge door.

Refrigerated and Frozen Ingredient Storage, FLOOR 1 (and again... oh well...)
Items: jar of yogurt labeled "OLIVES", (the pneumatic lift just backtracks you, intended to be a familiar theme in the Cake Factory)
Destinations: Dry ingredient storage

Dry Ingredient Storage, FLOOR 1
Items: "Sword" ice skates
Destinations: Warehouse

Warehouse, FLOOR 1
Destinations: Garbage/Junk pile, Shipping & Receiving
Puzzle: The perfect IT cake

Puzzle explanation: The perfect IT cake
Follow the IT department's directions to assemble "the perfect IT cake."
The resulting cake should have one decoration on top, one top layer, one (or two) middle layer(s), and one bottom layer.
The "potato" middle layer is optional, since you can also use the door code from Design or Accounting.
The final result should be:
Decoration: is Neo from The Matrix...
Top layer: is mint chocolate chip ice cream...
Middle layer: is white vanilla bean with seasonal mixed berry filling...
(Optional middle layer): potato, mashed and buttery and perfectly seasoned...
Bottom layer: German Black Forest dark chocolate gâteau...
...and this (finally) grants access to Management.

But first, we'll continue to explore downstairs, outside...

GARBAGE / JUNK PILE, OUTSIDE
Items: 25 Trillion Tonnes of Antimatter
Puzzle: Dumpster diving.

Puzzle explanation: Dumpster diving.
Use the "X" from the "?name/object=X", if you still have your notes, to fill in the asterisks on the items here, including the antimatter.
This area was intended to have a lot more junk piled in, but I hadn't planned well enough around it before the event needed to go live.

SHIPPING & RECEIVING, FLOOR 1
Destinations: Alleyway

A LONG ALLEYWAY, OUTSIDE (Start)
Items: "Magic Missile" Rockets 1-13
Destinations: continue down the alleyway
Puzzle: As explained in "The hintbook" comment on the giveaway page, most of the rockets are unnecessary (and probably useless) unless something happens that breaks the alleyway (this didn't happen).

A LONG ALLEYWAY, OUTSIDE (the main portion of the alleyway...)
Destinations: continue down the alleyway

A LONG ALLEYWAY, OUTSIDE (End)
Items: mass driver
Destinations: Parking garage (also accessible from Management)

PARKING GARAGE, OUTSIDE
Items: red/black keycard, black/black keycard

Okay, that's it for outside... back indoors, back to floor 2, back to delivering the cake to IT...

MANAGEMENT, FLOOR 2
Items: keycard, elevator
Puzzles: Infiltration

Puzzle explanation: Infiltration
This seems to be one of the more difficult puzzles for some reason. A part of that is likely due to an unconventional presentation of SGTools codes.
The keycard you are given here, combined with the elevator, takes you (again) back to the Lobby. From a story perspective, this gives you a credible excuse to use Management's elevator.
Instead of using the keycard given here, you're intended to use the red/black keycard that Xanadu swiped and gave to you in the parking garage.
But it doesn't work. The last Manager suggests a solution if you have a non-working keycard, referencing "some parts" of the keycard printed the wrong way around.
This wasn't very clear, apparently, so two hints were added to "The hintbook" comments. The second hint references one of the first puzzles, where a code needed to be "mirrored" in the restroom.
The first hint gives you another non-working keycard for the Packaging Department, although you already have the SGTools link for that room. Comparing your known-good Packaging Department code with the new keycard, you should hopefully understand how to "flip" a part of the parking garage keycard over to get it to work.
If these instructions are still too unclear, let me know!

And that brings us to the final act... where practically everything gets spoiler tags! :D

Act III: Level 3

"MAINTENANCE" / SECURITY, LEVEL 3
Puzzles: Survive an interrogation...

Puzzle explanation: Survive an interrogation...
As Xanadu suggests, avoid the truth, and convince them you belong there.
There are four ways to handle the interrogation.
You can play innocent, tell the truth, make up an excuse, or be completely uncooperative.
Blatant spoiler for the puzzle: Always pick option C.
Surviving the interrogation leads you to...

PROPRIETARY RECIPE TESTING LABS / RESEARCH & DEVELOPMENT, LEVEL 3
Items: Geodesic Energy Module (G.E.M.)
Destinations: WSC

WEAPONS SYSTEMS CONTROL, LEVEL 3
Items: left panel, right panel, food dish
Puzzles: Feed a cat

Puzzle explanation: Feed a cat
Note the name of the cat: Olive.
(Labs) The labs had an "empty container that says it contained olives" in their fridge, hopefully jogging your memory if you forgot about the other one.
Use the jar of yogurt labeled "OLIVES" from Refrigerated Ingredient Storage.
Put the yogurt inside (the middle of) the food dish, and set the food dish between the two panels.
Feeding the cat leads you to...

DEFENSIVE PERIMETER (Ledge), LEVEL 3
Items: black-striped slot on a black plinth
Puzzles: Keycards and Elevators, Part 2

Puzzle explanation: Keycards and Elevators, Part 2
Taking a cue from the coloring of the plinth and its stripes, use the appropriate keycard in the slot.
Insert the black-striped black keycard into the slot.
Activating the elevator leads you to...

FROZEN LAKE'S EDGE, DEFENSIVE PERIMETER (base), UNDERGROUND CAVERN
Items: Path forward (in many different directions)
Puzzles: Follow a map

Puzzle explanation: Follow a map
You need five cardinal (N/E/S/W) or ordinal (NE/SE/SW/NW) directions.
Hopefully, something you picked up along the way looks promising, and was probably suspicious when you first saw it.
Use the swirling set of characters from the decorating room to guide you. (You have a roughly 50/50 shot at getting it right.)
If you don't get lost in the pastry canyons, you encounter...

ICY CANYONS, UNDERGROUND CAVERN
Items: fight... with a sword?, run... or use magic?
Puzzles: Fight or flight?

Puzzle explanation: Fight or flight?
Another one that people understandably had trouble with, in part due to the slightly different formatting of the clues.
Both Xanadu's and Zenaye's suggestions are helpful.
Zenaye suggests fighting with a sword. Combining the fight link with the only sword you've encountered gives part of the code.
I probably should have formatted the ice skates as ?-C-- instead of just C, or something like that.
Xanadu suggests magic and running. Although many people immediately thought of using the Fireball (fire to fight fire?), the correct items are...
...the "Magic Missile" rockets. Combine the remaining two rockets (12 and 13) with the run link.
Now you have two codes...
...and they fit together, the rockets being placed on either side of the ice skates.
Figuring out whether to fight or flee (or both?) leads to...

FROZEN LAKE'S EDGE, DEFENSIVE PERIMETER (Base), UNDERGROUND CAVERN
Items: Elevator chain
Puzzles: Impromptu elevator

Puzzle explanation: Impromptu elevator
You need two items to solve this dilemma.
Grasp the chain with the Járngreipr dough hook...
...and pull out the Lúin thermal lance to begin weakening the elevator chain's weld.
Bringing you to...

DEFENSIVE PERIMETER (Ascent), UNDERGROUND CAVERN
Items: Flames
Puzzles: Don't die.

Puzzle explanation: Don't die.
You don't really have a lot of items left to use.
Flames are hot.
People seemed to have been waiting to use this item... the...
Svalinn heat shield.
And now, back to...

WEAPONS SYSTEMS CONTROL (Damaged), LEVEL 3
Items: nuclear fission machine, icosohedral socket
Puzzles: Either Assemble a geocidal device OR Power on a suit

Puzzle explanation: Assemble a geocidal device
This requires five components.
If you haven't found all five, you can find them via a "Behind the Scenes" map by solving the other puzzle instead.
(Although it's technically reasonably brute-forceable just before you enter Maintenance/Security.)
The five components needed are...
One microscopic black hole, found in Accounting
One solar oven, found at the Ovens
One mass driver, found at the end of The Long Alleyway
25 trillion tonnes of antimatter, found in the Garbage / Junk Pile
and lastly -- one nuclear fission machine, found here.
This leads to (the next room listed here).

Puzzle explanation: Power on a suit
Pretty simple, and you don't have many items left.
The socket is shaped like an icosohedron.
You have a Geodesic Energy Module from the Labs.
Insert the G.E.M. into the armor socket.
This leads to "ICY CANYONS, UNDERGROUND CAVERN, FAR EDGE" (skip the next two rooms).

WEAPONS SYSTEMS CONTROL (DAMAGED), LEVEL 3
Items: a blue fish on an elastic string, attached to a plastic yellow rod, and Olive the cat
Puzzles: paws of destruction

Puzzle explanation: paws of destruction
Combine Olive the cat with the cat toy, and she will assist in pressing the button that activates the geocidal device.
This leads to...

The Afterlife
The End. ("the bad ending")

Or, if you did the simpler puzzle from WSC instead, you would arrive at...

ICY CANYONS, UNDERGROUND CAVERN, FAR EDGE
Destinations: Lobby

LOBBY, FLOOR 1
Items: "Facade" magazine
Puzzles: spot the difference

Puzzle explanation: spot the difference
It's exactly the same as the Lobby from the beginning, I don't know what you're talking about.
Oh... yeah, except the receptionist is reading a very slightly different magazine.
Borrow her magazines, and read them (on the comfortable couch, if you choose to).
This (finally) leads to...

VISITOR'S HALL / MUSEUM, FLOOR 1
The End. ("the good ending")

Wow. This was really huge, you must have spent a lot of time building it. Too bad I felt it to be too much for me, thus I stopped in the bathroom. Thank you for the great experience you offered!!! :D

Oh, I see now!
I have found the sword, but have discarded it the moment I saw the code... X)
Okay, I will go beat him some more... someday. ;D

Thanks for great fun! :3

While I might be bummed I didn't actually manage to win anything (even though the most games I entered had under 20 entries total, just my luck heh) it was still insanely fun to do this. I can't even imagine how long it must have taken you but you bet I would 100% join any other adventures were you to do more in the future again :D