I have a decent understanding of Python but haven't learned Java, so I can't program any of this. However, I would be more than willing to make the textures/sounds/gui/etc. for everything (if these are actually good ideas and labor is the issue.) I imagine there will be a chunk of these ideas that are dead ends, but I wanted to show the whole concept.
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Lead: New ore. Macerated into Lead Dust first or directly smelted into Lead Ingots like other metal ore. Ore rarity would have to be balanced, but I would guess slightly rarer than Iron.
An alternative formula for the RE Battery is replacing the 2 Redstone with 1 Lead Plate + 1 Lead Dust. (Technically would require acid, but this is simplified)
Add Lead Dust to the Painter formula for drastically more uses. I.e. Painter+Dye+Lead Dust.
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Lathe: With the advent of machining, fine metal workings were easily produced with the Lathe (and other machining tools, but sticking to Lathe simplifies it). By putting Bronze or Refined Iron ingots into the Lathe, it produces 4 "Fine Metal Parts". Various arrangements of Fine Metal Parts on a crafting table can make musket parts, locks & keys for doors/chests, gas lamps, wall clocks, Metal Fishing Rods, etc.
Since Lathes techincally only work for symmetrical objects, this could be more accurately renamed to generic "Machine Tool", but that might be confusing for some (especially with "Machine Blocks").
Retort: Visually fits in with the new Brewing Stand. Crafted with a recipe of only glass (Retort shaped). Works like a furnace, burn something in the bottom slot to fuel it. Above has two slots, one for the item you want processed and one for empty cells (only used when processing gas). Produces 1 Charcoal per Wood Stick.
By processing Coal in the Retort, Coke Fuel is made, a much more efficient fuel source for Furnaces and Generators, ~x2 better than Coal/Charcoal.
The Retort can create gas by placing Empty Cells in one slot, and Wood Blocks, Coal Dust, or Coke Fuel in the other. This fills the cells one at a time, creating Gas Fuel Cells.
Electric Retort: Crafting an Electric Retort requires an Electric Circuit above, and a Refined Iron on either side of a plain Retort. The Electric Retort not only works faster, but can also process Sugar, creating 2 Charcoal per Sugar. Could look like a more metallic textured Retort, or it could be a block machine like Macerator etc.
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Stone Bowls: Same recipe as Wooden Bowls, but with Smooth Stone. Can be used for Mushroom Soup. Reason is: you can find mushrooms underground but couldn't eat them without wood, strange. Also it would be silly to be able to make a stone bowl for Mortar & Pestle but not for soup.
Mortar & Pestle: Crafting recipe: Smooth Stone bowl shape with a Cobblestone in the center and a Stick above that. Alternatively put a Stone Bowl on the bottom, Cobblestone in the middle, and a Stick on top. A primitive Macerator used by hand. Meaning you put it in a crafting grid with whatever you want to grind. Can't grind most metals, but can make: Coal Dust, Lead Dust, and Gold Dust.
Grind up any type of mushroom into "Mushroom Paste", which can be added to Bread in any crafting grid to improve it. Grind Cactus into "Cactus Paste" which can be eaten for a small hunger improvement, or put in Water Mills for a small boost (possibly other water-related recipes). Grind Seeds (wheat seeds, melon seeds, or pumpkin seeds) into "Seed Paste" which can be used the same way as Mushroom Paste (added to bread). Dandelion (Yellow Flower) can be ground into "Herbal Remedy" which cures Food Poisoning and Spider Poison.
All Mortar & Pestle recipes can later be made with the Macerator, though slower, requiring electricity, and not portable.
(Also, Mushroom and Seed Pastes can be eaten on their own but provide the smallest amount of hunger relief, less efficient than adding it to bread, and much less than eating Cactus Paste.)
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Musket: For ranged tools we go from bow and arrow straight to a mining laser, so muskets are step between (then possibly better guns). Long barrels made from 3 "Fine Metal Parts" in a row. Short barrels made from 2 "Fine Metal Parts" in a row. Determines if it's a pistol or rifle. Flintlock made from 1 "Fine Metal Part" and 1 Flint. The recipe is then: Flintlock Rifle: Wood Plank, Flintlock, and Long Barrel in a row. Or Flintlock Pistol: Flintlock with a Stick below it and a Short Barrel beside it. Muskets are either "(Loaded)" or "(Empty)", to load the musket you have to combine it with a Musket Cartridge, on a crafting table or in your 2x2 inventory crafting slot (like making a torch). So using it in combat requires firing, going into inventory, putting the rifle and ammo in the crafting slots, then putting the loaded musket in your hand, and firing again. Don't drop anything! The difference between rifle and pistol is accuracy. The pistol is good for basic range, but the rifle can also kill from afar.
Musket Cartridge: Gunpowder+Paper+Lead Ingot creates ~10 musket shots.
Locking doors+keys: Locks can be added to a chest or door of any type by combining them on a crafting table (i.e. Wooden Door+Lock). Keys are universal for all your locks, but are unique to you the player. With a key in hand, right click the chest or door (which has a lock added) to lock/unlock it. Basic ownership scripting to keep it unique to the player.
Gas Fuel Cells: Created with a Retort. Each cell lasts a long time, so a full stack of 64 lasts a really long time.
Gas Lighting: A step up from torches. The lamp itself is made from Fine Metal Parts. Place Gas cells in just like you would a Furnace. The lamp will burn the gas to produce light. The lamps can be toggled on and off (either by clicking or with redstone power source).
Visually, the lamps are similar to Torches but larger (and look like lamps, obviously), sticking to fence posts (iron/wood), walls, and floors. Changes to a slanted version vs. a vertical one when placed on walls. Also like torches--does not obstruct the player.
Vs. Glowstone it provides brighter larger radius light, looks better, and doesn't require any physical space (no path blocking). Also, no Nether Portal required.
Wall Clock: Combine a normal "Clock" with 1 Fine Metal Part. Works the same as a handheld clock but mounts on your wall like a painting.
Metal Fishing Rod: Normal Fishing Rod recipe, but replace the Sticks with Fine Metal Parts. Works the same way but instead of 65 uses lasts 351 (5.4 times longer, roughly the increase from a wood pickaxe to a Bronze one).
Metal Treetap: Same as a wooden Treetap for rubber extracting, but is built with Fine Metal Parts and lasts ~5.4 times longer. Can also be used in Extractor and Mining Pipe recipes (though wood is cheaper).
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Radiation: Nuclear Reactors and radioactive material (uranium ore, uranium, uranium ingots, uranium blocks) emit varying levels of radioactivity. Could be as simple as the electric shock that uninsulated cables give. It would be cool if the craters of nuclear explosions would emit radioactivity too, but probably too hard to code.
Lead Plate: Add to your Nuclear Reactor along with cooling cells etc. to prevent any radiation from escaping. The plates can't absorb much heat before melting so keep them isolated. Possibly requires 1 in each corner to block radiation? Otherwise don't go near the reactor core without a hazmat suit on. Unsure of exact cost from Lead Ingots. Probably 3 in a row, or two rows of 3 (6).
Hazmat Suit: Crafted in the shape of torso armor with Rubber in each corner (4), Lead Plating on both sides and bottom (3), and Advanced Alloy in the center (1). Protects the wearer from all radiation and can't be set on fire (still takes lava and drowning damage). Breaks easily (as any kind of tear or hole would compromise your protection). Advanced armors like Nano/Quantum could potentially block Radiation too.
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New Machines:
-Lathe (or "Machine Tool")
-Retort
-Electric Retort
New Objects:
-Lead Ore
-Lead Ingot
-Lead Dust
-Lead Plating
-Coke Fuel
-Fine Metal Parts
-Wall Clock
-Flintlock Rifle
-Flintlock Pistol
-Flintlock
-Long Barrel
-Short Barrel
-Musket Cartridge
-Lock
-Key
-Gas Lamp
-Gas Fuel Cell
-Hazmat Suit
-Metal Fishing Rod
-Mortar & Pestle
-Stone Bowl
-Mushroom Stew (Stone version of graphic)
-Mushroom Paste
-Seed Paste
-Cactus Paste
-Herbal Remedy
-Bread + Paste