The in-game handbook is long, and a lot of the guides get opened once. These are the parts that are actually useful later.
Things on the ground
Before you have chests, a lot of items can sit on the ground. Pots, bowls, crucibles, shoes, and similar things go on a flat block: up to four, one on each quarter. Hold the item, press Shift, and right-click. An empty hand picks it up with the same button.
Tools do not stand on the floor. Lean them on a wall, no more than two per block: Shift, Ctrl, and right-click the floor next to the wall. If an item can be stored this way, its handbook page says so.
Knapping
Flint goes on the ground with one Shift and right-click. Any other hard stone takes two. Orange marks the spare stone. You do not have to clear every orange voxel: the ones touching the future tool head are enough, and the rest falls away. A loose stone already on the ground can be knapped where it lies, if you have another suitable stone in hand.
The prospecting pick
A copper prospecting pick does not point at the vein under your feet. In Density Search Mode it measures how much ore is in the area. Break three stone blocks, at least 3 blocks apart and no more than 16. The chat then lists the ores and how much of each is around. A reading covers the whole height of the world, so a sample above ground and one below it say the same thing. The next one is worth taking 30 to 100 blocks away.
A low reading means the spot is poor, or you are on the edge of a deposit and should move. A high reading means the ore is nearby, not that it is in that exact block. A word like "ultra high" is judged against how much of that ore usually exists. Cassiterite in a good spot can still read 0.3‰, about 0.3 blocks of ore per 1,000 stone blocks, and for tin that is already an excellent reading.
The second mode, Node Search Mode (Short range, exact search), is turned on with the tool mode key while the pick is in hand. It looks much closer. If it finds ore, a vein is definitely inside the radius set for the world: 2, 4, 6, or 8 blocks. What remains is working out which way to dig.
Note: if the world setting Prospecting Pick node search radius is set to Disabled, the pick does not have this mode.
The rock on top
Sedimentary rock, including limestone and chalk, sits above metamorphic and igneous rock. If the top stone is igneous and it is not basalt, there is no limestone underneath. Basalt is the one that can sit on top of anything. Climate does not place limestone or chalk. The layer is there, or it is not. If the top stone is sedimentary, or it is basalt, more sedimentary layers can sit below, and a cave is where you see them. Marble only occurs as deposits inside phyllite or slate.
The charcoal pit
Charcoal is burned in a pit of blocks that do not burn and do not let air through. Any size up to 11×11×11 works, and 2×2×2 is enough to start. Fill it with complete stacks of firewood, with no empty blocks, and cover it completely. Leave the top of one stack open to the air, build a firepit there from dry grass and 4 more firewood, and light it. That opening has to be covered with a solid block within 30 in-game minutes. If the pit smokes quietly, the charcoal is ready in less than an in-game day.
Note: the pit walls must be made of non-combustible materials, and there must be no empty spaces inside to prevent the firewood from burning completely to ash. If you can hear the fire still burning inside, open the pit and extinguish it.
Later, a kiln door or an iron hatch door can stand in for a solid wall. Closed, they keep the pit sealed, and you can still get at the charcoal.
Rain
Rain wets farmland. It also puts out campfires, torches, and forges, and it cools hot items in a forge and on an anvil. A torch lights a drowned block again.
Fruit trees
They grow slowly and do not jump to full size the way ordinary trees do. Fruit comes once a year, and the month depends on the tree. A cutting goes into the ground, or onto a trimmed branch of another fruit tree. Grafts often fail. A cutting planted in soil fails more often still.
Dye without a mordant
Ordinary cloth sits in a mordant first: the material is ground and sealed in a barrel of water. Woad and tannin dye on their own, with no mordant. That is the way through before you have a pulverizer. A lot of the finished clothes are then sewn by a tailor.
Livestock and bees
Pigs, sheep, and goats eat from a large trough. Chickens and hares eat from a small one, filled with grain. A pair with enough food produces offspring, and the feed keeps animals from losing weight in winter. Chickens need a rooster and a henbox. An egg laid on the ground can be eaten, and it will not hatch. By the third generation the animals lose their fear, and a cleaver kills them outright. Ewes and nannies can be milked after they have given birth, and the more domesticated they are, the more often there is milk.
Honey and wax come from skeps that wild bees move into. They need flowers nearby, or the swarm will not settle. A populated skep goes into a free backpack slot with a right-click, and comes back out once that slot is selected with Ctrl and the mouse wheel. A mature skep is broken for the honeycomb, and the bees get angry. Something nearby that could be mistaken for you draws them off. Squeeze the honeycomb over an open container: the honey runs out, and the wax stays.
Elk
A rideable elk starts as a calf caught in a crate trap, then fed well for a year. After that it is half-tamed: saddle it and ride until it settles. An adult can be bought from the treasure hunter trader after the first story quest.
There is no riding without a saddle. A snaffle bridle handles like your own character. A curb bridle needs one press forward, and the elk keeps walking. A bone flute calls it to you while it is in a loaded area. Behind the saddlebags, on the right, are three slots for temporal gears.
The boat
A sailboat starts with five roller logs in hand. A blueprint appears in the world. The tool mode key turns it. The blue strip of that blueprint has to sit in the water. Logs and planks are one wood. With the block help on, the boat shows what it still wants: more firewood, two plumb and squares, and a coil of rope. Once it is in the water, ratlines let you climb the mast. A finished boat comes apart with a saw: hold right-click, and some of the materials come back.
The windmill and the helve hammer
A wooden windmill rotor needs at least 5 blocks of vertical room, and it catches more wind the higher it sits. Every 4 windmill sails add another 20% of power. Two windmills belong at least one and a half diameters apart, or they interfere with each other. Later, a metal windmill rotor with large windmill sails can be up to twice as wide. A small water wheel turns in a fast current, and those streams show up in hills and mountains.
A quern is made from igneous rock: granite, andesite, basalt, or peridotite. If the output slot is full, the flour drops on all four sides. A block beside the quern closes that side, and the grinding gets worse.
A helve hammer smiths plates, works iron blooms, and hammers blister steel into ingots. It does not smith tools or weapons. The anvil has to be bronze tier or better, and it sits three blocks from the hammer base.
The beehive kiln
Place a kiln door and press Ctrl and right-click: a ghost-block blueprint appears. The inside is 3×3×3. The floor is nine refractory gratings, and each one needs a pile of fuel under it, even a small pile. The three walls without the door get iron hatch doors. The finished pieces come out hot, and wooden tongs are what pick them up. Ordinary fireclay brick works here too, and it wears out sooner.
Open hatches let more air at the fuel, and the clay comes out darker. One clay can give as many as four colors this way. Fuel burning in all nine spots at once wears the bricks faster, so the piles should hold only what the batch needs.
Quenching
Quenching and tempering apply to iron, meteoric iron, and steel. Copper and bronze gain nothing from it. While the hot piece is in the temperature range on its tooltip, put it in water with Shift and a right-click. A coat of fire clay beforehand adds durability. Quenching without the clay raises the power tier.
Each later quench gives less and is more likely to crack the piece. Tempering brings that chance down: heat the piece less, and let it cool in the air, in your hands or on the ground, rather than in water.
These notes are from the handbook guides Ground Storage, Knapping, Prospecting, Rock Strata, Charcoal burning, Weather, Fruit Trees, Dye Making, Animal Husbandry, Tamed Mountable Animals, Shipbuilding, Mechanical Power, Beehive Kiln, and Quenching and Tempering.
Fishing
You need a fishing pole, bait, and a fairly large body of water. A puddle is unlikely to hold fish. Worms come from a worm grunting stick: a stick in the off hand, then Shift and right-click on bare soil. Not every block of dirt has worms. A wetter climate has more of them, cold weather has fewer, and in freezing weather they do not come up. Stink bait is cooked. Worms and stink bait both catch the smaller fish. Raw meat and small fish can be used as they are. With no bait at all, a bite still comes, and it takes a very long time.
Bait goes on the pole in the crafting grid, or with a left-click on the pole in your inventory while the bait is on the cursor. Cast with a right-click on the water. When the bobber goes under, right-click again to set the hook. The fish that lands in your inventory is dead. There is no way to catch a live one. Visible fish will take the bait if it lands close. Bites still happen where no fish can be seen. Freshwater and saltwater fish take the same baits and are caught the same way.
Worms catch smaller fish. Stink bait catches small and medium fish. The largest fish bite on meat or on a dead fish, with some exceptions. There are far fewer large species, so bait that only they will take runs into empty water more often. Juveniles, even of the large species, generally take the bait that smaller fish take. If a spot gives you juveniles of a large species, come back with meat, or with the small fish you caught there.
Each species lives in a climate range, and even there it does not cover the whole map. In a moderate climate, a spot with no fish is rare. At the hot extreme, and especially at the cold one, fewer species can live, and empty water is more common. Catch a large number in a short time and the spot is fished out. The population recovers, even after it has been fished out completely. Weather, temperature, and season do not change the fish, and the species in a spot stay the same over time. The game deliberately gives no message for a fished-out spot, the wrong bait, or water that never had fish.