As per previous messages, here is a horribly long list of bugs and tweaks that should probably be looked into:

Research Table and Aids:

• - Research aid items could be marked as such in their tooltip, like with Augmentation and Infusion Stabilizer items. Not sure whether this would be better for Augmentation, or whether the Infusion Stabilizer tooltop feature should be moved to Thaumcraft Fix instead.
• - Additionally, could research aid items placed in the world also be given a visual hint when they're accessible by a research table? Perhaps temphis runes floating around them, or maybe the enchanting table bookshelf runes particle effect?
• - Research desk doesn't look for aid blocks above/below itself, only in the exact y-level its on.
• - Fix portal (nether portal, end portal, crimson portal) research aid icon being invisible - maybe use vortex.png as the icon in this case as a generic image for all possible portals that can be used.
• - More ways to get fundamental theories - bookshelf research aid gives more fundamentals cards? Additional aids? New cards specifically for fundamentals?
• - Research card orders have a habit of being really shitty, you might start in one category and immediately get a bunch of cards that counteract your immediate progress. For example, I started researching alchemy and spent some fairly expensive cards to do so, but then straight after I got a card to discard alchemy research or split the progress with another useless category.
• - There's some unused research cards that might be worth adding.
• - Research cards which require essentia should blacklist essentia the player hasn't discovered (i.e. scanned in an item), to prevent cases where you need stupidly rare essentia from some addon mod and there's no way to get it, so you have to scrap everything and start again.

Thaumonomicon:

• - The research totals pop-up in the book still shows blocked research categories; they just all have a total of 0.
• - Probably worth also adding the improved flora images that I sent you before, if you don't wanna do this yourself I could try and make a PR for this.
• - I'm wondering if the changes made to research means that Crimson Rites are harder to get; as I recall they're supposed to drop with higher probability when you've started the appropriate research but I was having trouble getting them even with the research started. Has something broken here with the fixes made to research progression?
• - Perhaps make the crimson rites research only require a scanned copy of the book instead of destroying one; better for sharing in multiplayer.

Spells and Foci:

• - Water frozen by the freeze spell doesn't gradually crack and turn back into water like it should, it tends to get stuck. Sometimes this is due to light levels being too low, but it does also tend to happen during daytime anyway. May be something to do with block updates, as breaking the ice yourself tends to make ice around it also break.
• - Switching spell mode (like changing the size of the plan medium) is delayed after you press the button, though this might just be server lag. The lack of audio feedback probably doesn't help here, maybe have it play a "click" sound when pressing the button to help confirm that the button was pressed.
• - Unequiping spells doesn't work if you sneak-focus button in midair or while floating in water.

Misc:

• - Thaumcraft tools/armours don't have repair materials for the anvil. Very annoying if you want to repair a sword or some such.
• - If the Traveller's Boots run out of power, you still have step-assist to walk up one-block inclines.
• - The Traveller's Boots do not prevent the fall damage effect (screen tilt, bone crunch sound) even when they block all fall damage, very annoying when you're climbing around a forest.
• - Golem Use seals act weirdly in some cases, for instance I couldn't get a golem to fill up a bucket of water from a water source.

That's about all I remembered for now, if I find anymore I'll make sure to flood this issue with additional comments since brevity is for cowards.

Thanks for making this list, a lot of these are new bugs / problems so it helps a lot to have them here now :)

I am afraid I have more issues, these ones taken from an older list. Some of these may already have been solved, but there are some here that are definitely still a problem:

Art and Visuals:

• - Status effects that apply a screen shader fuck up transparency in things like the sun.
• - Salis Mundus particle effect doesn’t work for other players in multiplayer.
• - Entity aspect display likes to hang around after you put thaumometer away when the mob dies or you take away the thaumometer; particularly notable when smelting items with an Infernal Furnace, with the XP orbs that are created. The aspect display only goes away when you take the thaumometer out again and look back and forth a bit.
• - Flux Condenser “on” texture has a small error on it, where one of the pieces is missing a purple glow. Just a simple texture replacement, I can probably do this later.
• - Golem claw UVs are a bit odd on their ends, a simple model replacement would fix this. Again, I can do this and PR it at some point.
• - Readd runic shielding heart effect from TC4, if reasonable.
• - Tweak Thaumometer third-person holding position and animation (latter only if possible/reasonable); make the Thaumometer slightly bigger and with the lens facing the player model, and perhaps make the holding arm stick out too.
• - Additional flair for the Brain in a Jar: in older versions tapping it would make the jar tilt slightly, so if you get some time (ha) you could reimplement that effect.
• - Additional Thaumometer visual tweak to readd from Thaumcraft 4: make it so the player's hands can be seen holding the Thaumometer in first-person view, like with vanilla maps.

Audio:

• - One or two sounds seem to be client only, like Salis Mundus sparkle (the poof sound does work) or Golem Bell ring.
• - Arcane bore doesn’t make any rumbling sounds. Another client/server sound screw up?
• - Sounds in Thaumcraft have no or incorrect subtitles. Ones that use custom sounds lack subtitles, and ones that reuse vanilla sounds have incorrect subtitles (ghast fireball instead of arcane bellows for instance).
• - Readd runic shield hit sound when you’re hit, and for when it’s charging up.

Devices/Tools:

• - I’ve heard that magic mirrors and essentia mirrors make too much flux, “they should create flux based on amount transferred, not on transaction count”.
• - Automated Crossbows shoot custom arrows as regular arrows, as daedalus discovered when adding primal arrows to Wonders. Additionally, there’s also a note here that they like to shoot at nothing after a target dies.
• - Previously I found the cloudstepper ring double jump didn’t work on a server, may be due to a specific conflict somewhere since it works fine on the test server.
• - Similarly, I once had problems with boots of the traveller (and only these boots) not giving me a jump boost, again might be due to a mod conflict but I dunno what that would be.
• - Recharge Pedestal enhancement: make it produce a comparator signal based on how charged the item inside it currently is (percentage of current charge over the item's maximum charge of course).
• - Thaumometer shows entity aspects when it's placed in the first slot of the hotbar and when any other tool is selected. This doesn't happen if the Thaumometer is placed in any other hotbar slot.

Golemancy:

• - Golems in general have very bad AI, but the farming seal is one of note here, they seem to struggle with nether wart in particular.
• - Golem Traits are stored as numeric IDs instead of particular keywords, so when changing addons in a premade world, golem materials will randomly be shuffled. From the list of notes I have: “Causes client-server material ID desync with dedicated servers due to registration of vanilla TC materials being dependent on classloading of GolemProperties”.

Research:

• - Apparently research desks cause lag on multiplayer servers.
• - Give addons the option to not add an Observation and Theory research category if they add a new tab to the Thaumonomicon. I dunno how flexible you can make the API, mind you.
• - Revoking research doesn't seem to work, at least via the command. It looks like it removes the research, but upon clicking the entry that gets removed it just immediately gives itself to you again.
• - Headband of Curiosity can give you research items for categories that have been blocked.
• - Dragon Egg isn't detected as a research aid.
• - Any research (card or book entry) that consumes a phial of essentia should give an empty phial back.

Taint:

• - Flux phage is transmitted by everything, even things like the invisible mob ghosts added by EvilCraft that are left when mobs die, which makes containing the spread of the disease way harder than it needs to be. A blacklist to prevent certain mobs from getting flux phage/flu would make sense here.
• - Tainted Soil always changes back to dirt, even if it was originally sand or some such. I don’t know if this applies to other tainted blocks like tainted logs or not.
• - Taint can corrupt any mob that isn’t undead from what I know (apparently spellbats can be corrupted), so a tweak to ensure certain things can’t get tainted would be good.
• - Tainted Sheep should have their wool coloured purple. Wool placed down that gets tainted should also turn purple.
• - Flux Phage sometimes doesn't go away when it runs out on level 1 and turns into Flux Flu. Seems to be a client/server syncing issue, doesn't always happen.
• - Thaumic Slimes (when they do actually spawn) have green particles when they hop around, rather than purple ones.

Balance:

• - Overpowered Void Robes and Thaumium Fortress Armour, as I recall we discussed this previously.
• - Flux Spell effect may also be overpowered. Dunno how best to nerf this without making it useless next to other spell effects.
• - Thaumium Fortress Armour Masks could do with a buff, warp is ok but maybe a small boost, goggles are goggles, and the other two could definitely do with improving. Could even add new masks if that’s possible.

Misc:

• - Apparently Silverwood saplings grow into trees with trunks that can break through bedrock. This might have been fixed already though.
• - The /thaumcraft command used to have tab autocomplete functionality in 1.10, but got broken in the switch to 1.12.
• - In larger modpacks with custom potion systems, potions dropped as loot from things like urns or pech trades can bug out, giving you a purple and black cube that you can drink to give you absolutely no effects. I think Bewitchment was the one causing these bugged potions to appear, since they were called ‘Witch’s Brew’.
• - Focus projectiles can be shot straight through mobs that are very close in front of the caster.
• - Iron nuggets are added by Thaumcraft even though iron nuggets are a vanilla item. Probably a leftover from older versions, so if possible then removing this would help remove useless content.
• - Quark Emotes don't play well with Thaumcraft armours (certainly Augmentation Robes of the Adept, like we saw in testing), with the player model moving but the armour not following.
• - Improve Hollow Hill spawning. For one, when spawning in snowy biomes they don't have snow generated on top of them. Additionally, changing them to spawn using more modern structure blocks instead of hard-coded spawns might also be a good idea. Finally, it could also be good to have the eerie biome appear around them, but this might be better saved for the other idea we discussed about making Hollow Hill spawns more modifiable by addons so more advanced changes can be done in Augmentation instead.
• - When using phials on banners to decorate them, the phial gets consumed entirely - it doesn't even give you an empty phial back. Not sure whether essentia should even be consumed at all, since jar labels don't work like that.

By the by, I've sent you a few things in DMs that might interest you.

Super thankful for 1fcdd38, I found it quite frustrating when playing.