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Introduction
Alchemy Redone Remastered is a complete overhaul of the Skyrim LE mod Alchemy Redone, a rebuild from the ground up. The framework is still the same: 

1. Break down ingredients to make reagents.
2. Combine reagents to make potions
3. ???
4. Profit!

But the underlying mechanics have been redone. The following will give you a better understanding of how things work.

Alchemy Redone is an alternate alchemy system that removes the need to blindly fumble around and experiment with ingredients to figure out which one does what. Ingredients can instead be broken down into reagents, which correspond to alchemical effects - each effect has two reagents (except for Restore Health/Magicka/Stamina, which have one each), so any ingredient can be broken down into 6-8 different reagents. Reagents can also be bought or found anywhere you can get ingredients. See Reagents and Ingredients for more details.

Alchemy in AR is accomplished via a number of portable tools - to use, simply activate them, then exit the inventory menu and a crafting menu will then open. There are four alchemical devices and two enchanting devices you'll need to make full use of this system: the flask, retort, crucible, mortar and pestle, arcane augmenter, and arcane tuner. All of these can be found as loot (usually carried by NPC mages), bought from alchemists, or crafted. See Alchemical Tools for more details.

Alchemy Redone uses invisible perks - they don't require perk points to acquire and they don't override or interact with the vanilla perk tree, so this mod is compatible with all perk mods and alchemy mods. The base perk for all three branches is Hobbyist; from there, the branches spread out with four perks on each, convening again at Gnosis, the "grandmaster" perk. See Perks for more details.

AR lets you make any vanilla potion/poison (including many that weren't craftable before, like Blood Potions), more powerful versions of potions that couldn't be bought, as well as 48 completely new ones. All the new potions (but not revised versions of vanilla potions), infused soul gems, and welkynd stones have been added to levelled lists, so you can find or buy them in the world. The exception is all Tier 6 potions and varla stones - they can only be crafted. See Potions for more details.

Important note: Due to the sheer number of new recipes, each of them has conditions - if you don't have at least one of the ingredients and the perk, they won't appear in the crafting menu. This is not a bug - it's intended to reduce menu clutter. I've included a full list of recipes in one of the articles.

Reagents and Ingredients
Ingredients are divided into six tiers, based on their rarity and potency. Tier 1 ingredients produce 1 portion of a reagent; the number increases as you go up, but so do the perk requirements. Reagents are miscellaneous items, so they can't be combined with ingredients, but they all have ingredient keywords, so they still work for sorting and they appear on the same levelled lists as ingredients. Each alchemical effect has two reagents (except for Restore Health/Magicka/Stamina, which have one each), and all vanilla ingredients can be turned into reagents based on their effects - so each ingredient can be broken down into 6-8 different reagents. See below for a complete list of ingredients by tier.

Some reagents can be created through other means: corundum, gold, iron, quicksilver, and silver ingots can be ground down to powder; salt can be ground into Fine Powdered Salt, and human and troll skulls can be ground into bonemeal; none of these have requirements. Alkahest and penicillium can be made with common items, and opium can be distilled from moon sugar; these require the Hobbyist perk. Mammoth tusks can also be ground into powder; this requires the Professional perk. Ingredients listed after the semi-colon belong to the CC mods.

Tier 1 (1 portion, Hobbyist): Common plants and small animals.
Antlers (large/small), bee, beehive husk, bird egg (all), butterfly wing (blue/monarch), canis root, charred skeever hide, dartwing (blue/orange), deathbell, dragon's tongue, elves ear, Felsaad tern feathers, fish (all), frost mirriam, garlic, giant lichen, grass pod, hanging moss, hawk beak/feathers/egg, honeycomb, jazbay grapes, juniper berries, lavender, mountain flower (blue/red/purple), mudcrab chitin, mushrooms (all), nightshade, nordic barnacle, salt pile, scathecraw, skeever tail, small pearl, snowberries, swamp fungal pod, thistle branch, torchbug thorax, trama root, tundra cotton, wheat.

Tier 2 (2 portions, Professional): Uncommon plants, common extraplanar flora, humanoids, large animals, uncommon materials.
Ancester moth wing, ash creep cluster, ashen grass pod, bear claws, boar tusk, dwarven oil, emperor parasol moss, giant's toe, gleamblossom, human flesh/heart, moon sugar, poison bloom, powdered mammoth tusk, sabre cat eye/tooth, yellow mountain flower.

Tier 3 (4 portions, Scholar): Uncommon extraplanar flora, magical flora, lesser monsters/undead (large, intelligent, or extraplanar, but not magical/magic-using; includes large humanoids like giants, ogres, minotaurs)
Ash hopper jelly, briar heart, chaurus eggs, netch jelly, nirnroot (green and red), spider egg, troll fat; dreugh wax, elytra ichor, lichor/ambrosia, kagouti hide, minotaur horn, ogre teeth, scrib jerky/jelly, scalon fins 

Tier 4 (6 portions, Expert): Mid-tier monsters/undead (Intelligent or magical/magic-using), lesser daedra 
Burnt spriggan wood, Chaurus hunter antennae, ectoplasm, glow dust, ice wraith teeth, spawn ash, spriggan sap, taproot; daedroth teeth, gnarl bark, heart of order, hunger tongue, imp gall, sload soap

Tier 5 (8 portions, Master): Greater monsters/undead (intelligent and magical/magic-using), greater daedra
Daedra heart, fire/frost/void salts, hagraven claw/feathers, vampire dust, wisp wrappings; daedra silk/venin

Tier 6 (10 portions, Grandmaster): Dragons
Dragon bones, dragon scales (these can ground into powder with the Scholar perk, but you have to combine the powder with ethereal dust and reduce the mixture with the crucible to get Draco Pulvis).

There's also a special reagent called ethereal dust, which is created by dismantling a magic scroll with the arcane tuner. Ethereal dust is used to combine filled soul gems, infused magic into soul gems, and create welkynd and varla stones. It cannot be bought, only crafted.


Alchemical Tools
As mentioned above, AR makes use of five different apparati and tools. You can buy them premade at any apothecary (which costs a lot), buy set of schematics (which costs less, but also requires raw materials), or craft them yourself (the cheapest option - it requires only the raw materials and a forge - but you also need Smithing 20). All tools are sold by apothecaries and khajiit caravans. The table below lists the tools, their functions, and material requirements.

* Alembic Breaks down potions/poisons into reagents2 iron ingots, 2 glass
* Arcane augmenter Combines and infuses soul gems2 dwarven ingots, 1 lesser soul gem
* Arcane tuner Breaks items down into ethereal dust2 dwarven ingots
* Crucible Breaks down ingedients into reagents1 steel ingot, 1 corundum ingot
* Mortar and pestleGrinds up various substances1 quicksilver ingot, 1 steel ingot
* RetortMakes and combines potions/poisons2 glass


Perks
In Alchemy Redone, there are three "branches" of the Alchemy perk tree: the potion branch, the reagent branch, and the experimenter branch. Each is explained below. The Alchemy number listed in parentheses after each is the skill level required to acquire the perk(s) in question. You can gain all the perks by writing a treatise or thesis (see below) using the tanning rack; this requires leather, paper rolls (increases by level), and an inkwell (which can be crafted too).

Hobbyist
Hobbyist is the "base perk" that leads into all three branches.

Hobbyist (Alchemy 0):  Create Tier 1 potions and poisons, and break down Tier 1 ingredients into reagents. Create long taffy treat.  Requires an Alchemist's Treatise I.


Reagents/Potion Making
These perks are listed together because they are acquired at the same time. The first perk listed in each pair grants the ability to break ingredients down into reagents: as ingredients become more powerful, it requires more knowledge and care to properly extract their essence. The second perk covers potion-making: as with reagents, each one grants access to more powerful mixtures, as well as unique potions and poisons. 

Professional/Medicinal Alchemy (Alchemy 20): Break down Tier 2 ingredients and Tier 1 potions into reagents. Grind mammoth tusks into powder. Create Tier 2 potions and poisons; combine Tier 1 potions and poisons. Create blood potions and stamina chew. Requires an Alchemist's Treatise II.

Scholar/Malefactor (Alchemy 40): Break down Tier 3 ingredients and Tier 2 potions into reagents. Create Tier 3 potions and poisons; combine Tier 2 potions and poisons. Create concentrated frostbite venom, concentrated mystic venom (CC version only). Requires an Alchemist's Treatise III.

Potions Master/Theoretician (Alchemy 60): Break down Tier 4 ingredients and Tier 3 potions into reagents. Grind dragon bones/scales into powder. Create Tier 4 potions and poisons; combine Tier 3 potions and poisons. Create a bezoar. Requires an Alchemist's Treatise IV.

Grandmaster/Dark Potions (Alchemy 80): Break down Tier 5 ingredients and Tier 4 potions into reagents. Create Tier 5 potions and poisons; combine Tier 4 potions and poisons. Create creeping doom poison. Requires an Alchemist's Treatise V.

Experimenter
The Experimenter perks represent an alchemist pushing the boundaries of what's possible - merging soul gems and infusing spells or magicka into them to create magical items.

Experimentalist I (Alchemy 30): Combine soul gem fragments to make petty soul gems; break down soul gems of any size into fragments; reduce Novice scrolls into ethereal dust. Requires an Experimenter's Thesis I.

Experimentalist II (Alchemy 50): Combine petty soul gems to make lesser soul gems; reduce Apprentice scrolls into ethereal dust. Create welkynd stones. Requires an Experimenter's Thesis II.

Experimentalist III (Alchemy 70): Combine lesser soul gems to make common soul gems, or filled petty soul gems to make filler lesser soul gems; reduce Journeyman scrolls into ethereal dust. Create infused soul gems (see below). Requires an Experimenter's Thesis III.

Experimentalist IV (Alchemy 90): Combine common soul gems to make greater soul gems, or filled lesser soul gems to make filled common soul gems; reduce Expert scrolls into ethereal dust. Create black soul gems. Requires an Experimenter's Thesis IV.

Gnosis
Gnosis (Alchemy 100): Gnosis represents the pinnacle of alchemy, a culmination of all your studies and experiments. 

Break down Tier 6 ingredients and Tier 5 potions into reagents. Create Tier 6 potions and poisons; combine Tier 5 potions and poisons. Combine greater soul gems to make grand soul gems, or filled common soul gems to make filled greater soul gems; reduce Master scrolls into ethereal dust. Create varla stones; repair flawed varla stones (CC patch only). Create Broluses' Marvelous Elixir. Requires a Grandmaster's Thesis.


Potions
Like reagents, potions are divided into five or six tiers of magnitude. You can make any standard vanilla potion (including the ones from the DLCs, as well as blood potions), along with a variety of new potions, listed below. Potions and poisons up to Tier 5 are sold by apothecaries and khajiit caravans, and can be found as loot in the same places you'd find vanilla ones. Babette (Dark Brotherhood) and Herluin (Thieves Guild) have special levelled lists, so they only sell reagents, tools, and new poisons, but not potions. 

Most vanilla potions and poisons can be broken down into reagents; you can also combine two lesser potions or poisons of Restore or Damage H/M/S to make a stronger version.

The following is a list of the new potions. The first table lists all the six-tier potions and poisons (the effects listed are for Tier 1 - just to give you an idea of what they do). The second lists unique potions and poisons, or ones that don't have six tiers. The perks required to make them are also listed.

Potions of regenerate HMS and the Thieves Guild potions (Conflict, Escape Larceny, Keenshot, Plunder) are craftable, but the recipes produce the vanilla version, not a new one. This is deliberate - the vanilla versions in this case are plenty powerful. A full list of recipes is included in the archive.

Affliction Poison * Damage Health 15 pts  
* Damage Magicka 15 pts  
* Lingering Damage Health 2 pts for 20 secs 
* Lingering Damage Magicka 2 pts for 20 secs 
* Damage Magicka Regen 100% for 20 secs

Agony Poison* Damage Health 15 pts  
* Damage Stamina 15 pts
* Lingering Damage Health 2 pts for 20 secs 
* Lingering Damage Stamina 2 pts for 20 secs 
* Damage Stamina Regen 100% for 20 secs

Armsman's Brew* Fortify Block 15 pts for 180 secs
* Fortify One-Handed 15 pts for 180 secs 

Burglar's Tonic* Fortify Sneak 15 pts for 180 secs
* Fortify Lockpicking 15 pts for 180 secs

Burning Blood* Paralysis for 2 secs
* Damage Health 4 pts for 5 secs
* Weakness to fire 40% for 60 secs

Conjurer's Potion* Fortify Conjuration 30 pts for 240 secs

Crippling Poison* Slow 50% for 15 secs
* Ravage Stamina 50 pts for 15 secs

Damage Health* Damage Health 4 pts for 5 secs

Damage Magicka* Damage Magica 4 pts for 5 secs

Damage Stamina * Damage Stamina 4 pts for 5 secs

Dampener Poison* Weakness to fire/frost/shock 50% for 40 secs

Despair Poison* Damage Magicka 15 pts  
* Damage Stamina 15 pts  
* Lingering Damage Magicka 2 pts for 30 secs 
* Lingering Damage Stamina 2 pts for 30 secs 
* Damage Stamina Regen 100% for 30 secs

Draught of Endurance* Fortify Stamina 25 pts for 180 secs
* Regen Stamina, 25% for 180 secs 

Elixir Vitae* Regenerate Stamina 30% for 180 secs
* Fortify Stamina 30 pts for 180 secs
* Regenerate Magicka, 30% for 180 secs
* Fortify Magicka 30 pts for 180 secs

Exhaustion Poison* Ravage Stamina 40 pts for 30 secs
* Lingering Damage Stamina, 2 pts for 30 secs

Fear* Fear L10 for 60 secs

Freezing Blood* Paralysis for 2 secs
* Damage Health 4 pts for 5 secs
* Weakness to frost 40% for 60 secs

Frenzy Poison* Frenzy up to L8 for 30 secs

Hunter's Infusion* Fortify Sneak 15 pts for 180 secs
* Fortify Marksman 15 pts for 180 secs

Hush Poison* Damage Magicka Regen 100% for 40 secs

Juggernaught Draught* Fortify Heavy Armor 15 pts for 180 secs
* Fortify Two-Handed 15 pts for 180 secs 

Magician's Extract* Fortify Alteration 15 pts for 180 secs
* Fortify Illusion 15 pts for 180 secs 

Monk's Tisane* Fortify Unarmed 15 pts for 180 secs
* Fortify Light Armor 15 pts for 180 secs 

Mute Poison* Ravage Magicka 50 pts for 30 secs
* Lingering Damage Magicka 2 pts for 30 secs

Nightingale Extract* Fortify Illusion 15 pts for 180 secs
* Fortify Light Armor 15 pts for 180 secs 

Paralysis Poison* Paralyze for 3 secs

Penumbra* Muffle 10% for 30 secs
* Invisibility for 30 secs

Philter of Flameward* Resist Fire 20% for 300 secs

Philter of Frostward* Resist Frost 20% for 300 secs

Philter of Shockward* Resist Shock 20% for 300 secs

Philter of Spellward* Resist Magic 10% for 300 secs

Potion of Alteration* Fortify Alteration 30 pts for 240 secs

Potion of Bull's Strength* Feather 50 pts for 300 secs

Potion of Defiance* Resist fire/frost/shock 15% for 180 secs

Potion of Destruction* Fortify Destruction 15 pts for 240 secs

Potion of Enhanced Stamina* Fortify Magicka 30 pts for 180 secs

Potion of Extra Magicka* Fortify Magicka 30 pts for 180 secs

Potion of Haggling* Fortify Barter 10 pts for 120 secs

Potion of Health* Fortify Health 30 pts for 180 secs

Potion of Healing* Restore Health 5 pts for 5 secs

Potion of Magicka* Restore Magicka 5 pts for 5 secs

Potion of Stamina* Restore Stamina 5 pts for 5 secs

Potion of Illusion* Fortify Illusion 20 pts for 240 secs

Potion of Invisibility* Invisibility for 30 secs

Potion of the Knight* Fortify Heavy Armor 15 pts for 240 secs

Potion of Light Feet* Fortify Heavy Sneak 15 pts for 240 secs

Potion of Lockpicking* Fortify Lockpicking 15 pts for 240 secs

Potion of Magicka* Fortify Magicka 30 pts for 180 secs

Potion of Pickpocketing* Fortify Pickpocket 15 pts for 240 secs

Potion of Stamina* Fortify Stamina 30 pts for 180 secs

Potion of the Berserker* Fortify Two-Handed 15 pts for 240 secs

Potion of the Defender* Fortify Block 15 pts for 240 secs

Potion of the Healer* Fortify Restoration 15 pts for 240 secs

Potion of the Warrior* Fortify One-Handed 15 pts for 240 secs

Potion of True Shot* Fortify Marksman 15 pts for 240 secs

Potion of Waterbreathing* Waterbreathing for 30 secs

Potion of Well-Being* Restore Health/Magicka/Stamina 7 pts for 5 secs

Sal Mirabilis* Fortify Enchanting 20 pts for 60 secs

Sal Sapientiae* Fortify Smithing 20 pts for 60 secs

Skirmisher's Potion* Fortify Light Armor 15 pts for 240 secs

Slow Poison* Slow 50% for 10 secs

Sorcerer's Unguent* Fortify Destruction 15 pts for 180 secs
* Fortify Conjuration 15 pts for 180 secs

Thunderstruck Poison* Paralysis for 2 secs
* Damage Health 4 pts for 5 secs
* Weakness to Shock 40% for 60 secs 

Tincture of Nightshade* Fortify Sneak 15 pts for 180 secs
* Fortify One-Handed 15 pts for 180 secs 

Vapors of Aetherius* Fortify Magicka 15 pts for 300 secs
* Regenerate Magicka, 15 pts for 300 secs

Vigilant's Elixir* Fortify Heavy Armor 15 pts for 180 secs
* Fortify Restoration 15 pts for 180 secs 

Wardancer's Libation* Fortify Destruction 15 pts for 180 secs 
* Fortify One-Handed 15 pts for 180 secs 

Woad* Fortify Light Armor 15 pts for 180 secs
* Fortify Two-Handed 15 pts for 180 secs 

Woodsman's Infusion* Fortify Light Armor 15 pts for 180 secs
* Fortify Sneak 15 pts for 180 secs


Potions from the CC/AE version

Cure poison has only one version, craftable with Medicinal Alchemy; the others are normal 6-tier potions.

Cure Poison* Cure poison

Light Potion* Light 40 ft for 90 secs

Nighteye* Nighteye for 5 mins

Spell Absorption* Spell Absorption 15% for 240 secs


Unique Potions/Poisons
Only one version of each of these exists; it can be made with the perk listed.

Bezoar* Immunity to poison for 24 hrs Theoretician

Blood Potion* As vanillaMedicinal Alchemy

Broluses' Marvelous Elixir* Restore H/M/S allGnosis

Creeping Doom* Fear up to L20 for 45 secsDark Potions
* Slow 50% for 45 secs

Conc. Frostbite Venom* Damage Health/Stamina 10 pts for 4 secs Malefactor

Conc. Mystic Venom** Damage Health/Magicka 10 pts for 4 secs Malefactor

Cure Disease* Cure diseaseMedicinal Alchemy

Healing Poultice* Restore Health 20 ptsSpecial**
* Regenerate Health, 10 pts for 300 secs
* CC/AE version only.

** Poultices are divided into nine tiers - I through IX. Tier I is craftable at Alchemy 0-20; Tier II at 21-30, etc., but they don't require any perks. These are also sold at apothecaries.


Infused soul gems, Black Soul Gems, Welkynd and Varla Stones

Varla stones are reusable soul gems; unlike the ones added in the CC content, they can hold up to grand souls. If you have the CC patch, you can also repair flawed varla stones to match the craftable ones. Welkynd stones are identical to the ones in Oblivion - they completely restore Magicka. Infused soul gems can be created with the Experimenter III perk; they let you add a magic effect to a soul gem, which can then be swallowed to grant a cloak effect - fire, frost, etc.
All of these recipes require the arcane augmenter.

Black Soul Gem* 1 grand soul gem, 5 ethereal dust, 1 daedra heart OR 1 human heart

Repair Varla Stone*1 flawed varla stone, 5 ethereal dust

Varla Stone* 1 black soul gem, 3 draco pulvis, 5 ethereal dust

Infused soul gems

Dragon* Dragonskin (Caster ignores 80% of all physical damage for 60 seconds)

Flame * Flame Cloak (Fire damage 5 pts for 90 secs)

Frost* Frost Cloak (Frost damage 5 pts for 90 secs)

Lightning* Shock Cloak (Shock damage 5 pts for 90 secs)

Poison* Poison Cloak (Poison damage 5 pts for 90 secs)

Shadow* Shadowcloak of Nocturnal (Invisiblity while sneaking for 90 secs)


Miscellaneous Items
Aside from all the potions, poisons, and soul gems, there are some miscellaneous items. These have no requirements to make beyond raw materials; the components and crafting station required to make each is listed below. Items marked with a star are decorative and serve no purpose.

Alchemical Scale*Forge2 steel ingots
Bain-marie*Forge2 dwarven ingots
CharcoalForge1 firewood
Dewar flask*Forge1 empty wine bottle
Draco PulvisRetort1 powedered dragon scale,  1 powedered dragon bone, 1 ethereal dust
Fractional distillation column*Forge1 corundum ingot + 2 glass
InkwellCookpot1 firewood, 1 iron ore
Long taffy treatCookpot5 snowberries, 1 honeycomb
Mycena Lux Aeterna samples*Workbench 1 glowing mushroom, 1 paper roll
Reagent crate*Workbench 3 wooden plates
Stamina ChewCookpot1 long taffy treat, 10 Vita


CC Patch
The CC patch requires the free DLCs Fishing, Rare Curios, and Saints and Seducers; it is compatible with a downgraded version of SE (with just the CC content) or with a full AE install. It covers all the new ingredients and potions added in those DLCs.

IJ Patch

The Immersive Jewelry patch changes the recipes for tools and apparati to use bars instead of ingots, and renames corundum to copper. It also adds recipes to grind down bars of copper, gold, iron, quicksilver, and silver to make 1 portion of dust. 


Known Issues
* The meshes for the crucible and part of the distillation column don't show up. They were made for Skyrim SE, but I ran them through Cathedral Optimizer; they appear in the CK, but for some reason they won't show up in game.


Credits/Thanks
QuantumButterfly, for the original Alchemy Redone mod.

scorrp10 and maxarturo, for help and advice with the new scripts.

More credits from the original readme:
FOEnthusiast for the original Chemistry mod, which was the inspiration and the blueprint for this mod.  If you don't like Alchemy Redone, check out Chemistry; it's fantastic!  

IndigoNeko and Is This Display Name Taken? for SkyRealism Crafting kits and Crafting Complete, respectively, the tool scripts of which were super-helpful in making the portable alchemy stations.

Oaristys and Tony67, whose Modders Resource Pack provides the meshes for the crucible, alembic, and potion box.

Blary's Alchemy Clutter Resource provides the mesh for the new flask, mortar and pestle, mushroom samples, and scales.