Tis100

Tunic, in a certain way.

Tunic?

• Tunic — You need to figure out the game's manual to know how to play. Souls-style exploration and combat.
• Papers, Please — If you liked Rocket Shop, you'll like this. You are a border guard, checking people's documents and choosing if they can enter. The rules change every day as international tensions grow. Great plot with multiple endings, expressed with just your green and red stamps.
• Hypnospace Outlaw (kind of) — You are a moderator in a fictional version of GeoCities in the last months of 1999. Your training is web pages and crusty point and click CD-ROM slideshows. It's heartfelt story about the impact of technology on society and a loving funeral for that era of the world wide web.

As even further stretches, there is TIS-100 and Shenzhen I/O, both Zachtronics games that have you do programming. The tutorial for TIS-100 just opens a PDF that looks like a crusty scan of an ancient computer manual, like you were learning to program on a C64 or something.

Strange Horticulture -You run an occult plant shop and identify plants by leafing through a botanical guidebook, matching illustrations and descriptions.

HighFleet - Intercepting enemy radio transmissions means using the in-game codebook and manual tables to decode messages and triangulate positions.

The Signal State - A Zachlike about repairing farm equipment with modular synth racks and lots of documentation.

Retro Gadgets - You build electronic gadgets from scratch, and reading the chip documentation is basically the whole game.

Sethian - You learn a dead alien language by studying an in-game dictionary/manual to converse with a computer.

Carrier Command 2 - Co-op crewing a carrier where the in-game manual is dense and necessary, giving strong Tin Can/submarine-crew vibes.

Objects in Space - Space sim, flying a submarine-like ship, reading dials and signals.

Jalopy - Roadtrip / car maintenance game set in Eastern Bloc.

Reentry - Crazy realistic space sim where you follow manuals, procedures, checklists etc to complete missions like the Apollo moon landing.

Dwarf Fortress

Caves of Qud

Cogmind

Tunic

EXAPUNKS!

It's the dialup 70s, your body is turning into computer parts, and medicine costs 300 dollars a day.

Read the zines, learn to hack. Hack a restaurant. Hack a bank. Hack your body. Hack the planet!

https://store.steampowered.com/app/370360/TIS100/

The instructions for this game come in the form is PDF written in an in-universe style.

The DS version of Ni no Kuni included a physical spellbook you're meant to consult. JP-only, but the fantranslation made it into a PDF.

Iron Nest? You drive a turret and you have to read instruction on how to operate it and where to shoot. Not yet come out though.

Papers, please kinda fits

I have a game wishlisted which I think needs constant consultation with diverse information to be played. It's called Comet64, and you kind of have to program a special kind of computer called Comet64.

Not quite as strictly as what you've cited, but some of the older Sierra point-and-clicks relied on maps/pamphlets/etc that were packed in with the game. Most just used them as low-budget and thematically in-universe anti-piracy gating (the Dagger of Amon Ra), but some stretched beyond that. Conquests of the Longbow: the Legend of Robin Hood had royal family crests, language keys, and (of I remember correctly) a catalog of gems that were all perused outside of the game interface.

GOG has PDFs of all those documents if you buy the games there, so you can still experience it fully. Might be worth checking out, since it's usually less than $5.

Subnautica and Subnautica 2.

The guide is an ingame tablet that's literally your character's survival guide book, recording data on wildlife and tracking your crafting tree.

Not really a manual, but more of a 4th wall derailment into a fever dream of sorts? With a lot of reading while navigating a mystery? And some match 3 tower defence action in between?

Titanium court.

For more of a game with an actual manual focus, try - King of the Bridge. It’s a game about chess. Mostly.

Mina the Hollower. Charming af!

I love Zachtronics games that have been recommended a few times already. But for a different genre...

Ni no kuni is a RPG that was kind of that, with a big (originally physical) book of magic. But since it's been remade on many platforms as a digital download, the book is there in a rather boring (but useable) pdf reader-like UI and has been made a bit less useful.

It's still rather charming having this in-universe codex-like book listing gameplay elements, items, recipes, bestiary, and bits of lore about the world (and some pages just telling random fables about whatever). Nowhere near required reading for the game though, just occasionally useful.

I haven't gotten to play it myself yet, and it may be more "meta" than you mean by this, but I understand that reading the original game's manual is a big part of the gameplay of The Remake of the End of the Greatest RPG of All Time.

Retro Game Challenge (English version of Game Center CX: Arino no Chōsenjō) and its excellent fan-translated sequel.

Ostranauts?

Its a space salvage game with a good atmosphere

For modern game, try elite dangerous. It doesn't come up with pdf (or I don't find it yet), but you have to do tutorials and watch a lot of YouTube to know how to fly your ship, especially without auto-pilot, auto-docking

https://store.steampowered.com/app/4209010/Lakehopper/

If by "in-game manual" you mean one that's part of the game world (not necessarily displayed on a computer screen) check out the classic Infocom adventures. For example, Border Zone came with a printed terrain map and tourist guide, and Sherlock and The Witness came with newspapers, among other things.

I believe in Deaths Door, we had to gather pages that explained the game mechanics, but by the time you got the pages it was moot point. Tho I might mixing up some games.

Still There

Give king of the bridge a check. Learning about the manual and working with it is the whole plan