Museum Heist Walkthrough

DECODING THE TOME

Pay attention to the carpets surrounding the main (black) room. Unlike the other rooms, this one has two colors in its carpet... The blue carpets represent Morse code! This is also hinted by the 'Dit' and 'Dah' in the staircase. The Morse spells out "Atbash", which is a type of substitution cypher. You can find a translator here: http://rumkin.com/tools/cipher/atbash.php
Eject the book, copypaste its contents into the translator, and you're on your way!

THE PURPLE ROOM

The first page of the book starts with "Behind me lies a meager pawn". Take it (a wooden button) from the shulker box behind the lectern. The checkered pattern in the purple room is labeled as "Modern Cantur". Cantur is an ancient form of Chess, which means that the 6x6 checkered pattern in the room represents a chessboard. But which heads correspond to which pieces? If you look at the statues in the cyan room, you'll see that the king has a cow head, and the queen has a pig head. That means these heads on the board represent the respective pieces. The horses represent knights, whose pieces are horse-shaped. The first page also says "place it somewhere safe" - that is, somewhere on the board where it can't get taken. There is only one such spot - third row from the top, second row from the left. Place the button there, press it and take your iron ingot. Also take the stick and 5x white wool from the chest, as well as the red wool from the barrel in the storage room.

THE CYAN ROOM

Press the button to play the song. You need to complete its second half. The song is Twinkle Twinkle Little Star, and to complete it right-click the blocks (from left to right) the following amount of times: 11 11 10 10 8 8 6. You will now get a bone. Craft the bone into bone meal, and that into white dye. Use it to dye the red wool white (this is the new recipe that was added), and craft a banner using the crafting table in the purple room. You can see that it can only be placed on Diorite blocks, and so you have to put it next to the statues in the cyan room. Once you do that, you get a gold ingot.

THE GREEN ROOM

Use the two remaining white dyes to dye both signs, revealing the text on them. This means that the [0 0] coordinate is at the bottom-left corner. Turn on the levers in the coordinates specified by the book, as well as the one shown in the purple room: [2 1]. You will then get a diamond.

THE GREAT ESCAPE

Go to the storage room, and put each of the minerals in the shulker box of the same color. For each one you deposit, two of the six lamps in the upside down room will start flashing. When you activate all three pairs, the lamps' pattern will represent the order in which you should press the buttons to open the safe. Except... you need to rotate it by 180 degrees. You're in the upside down room, after all.

Once you enter the safe and take the painting, you'll trigger the security mechanisms! To break your way out, use the gunpowder and sand to craft a block of TNT, and place it under the lamp. When the lamp turns on, the redstone current will also ignite the TNT, blasting the door out! Collect the fireworks and equip the Elytra, return to the main room, and fly back into the air vent to freedom!