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Scan the items, take the money and give the customer their change.

The sticky note on the computer screen will tell you how much each coin is worth.

You may have sequence broken the game. The "deliver running shoes" flag might've not registered because you gave Yuna her shoes before she even asked for them.

Kaede is still a work in progress character.

I would go as far as to say that our nightly interactions with her are not "canon".

Moondev will, most probably, announce the next release date two weeks prior to said release.

Tl;dr - It's done when it's done.

You have to go through all of the game's events, most of which requires fully maxed out relationship with Yuna.
The REC discord may or may not have a cheat code to unlock the gallery. 

Such adjustments can be made only after the game has reached a full release state.

Not anytime soon, unfortunately.

After you "win" the party event Kaede will have a chance to stay the night at Yuna's place, allowing you to bang her to your heart's content.

If you got for a run during the day you unlock the part time job, meaning you can work at night.

Currently, one shift gives you around 30000 credits, making the PeepTube coin conversion to credits kind of obsolete.

Moondev, the developer, rarely visits this page, no. The best way to actually reach the developer is on discord or subscribestar.

Currently, the story is full of holes. Kan is a member of the in-universe illuminati yet all he does is monitor the apartments of his appointed apartment building.

Dude has the key to the ultra secret underground facility yet he's no more than a footnote, currently.

After you go through the entire laboratory and learn "the truth" that's where story content currently concludes, yes.

To hold hands, select your hands (second option, unlocked from the start) and click on Yuna's arms while she is lying on her back.

To turn Yuna around you need to raise both of her arms with the first tool (also unlocked from the start).
Once both of her arms are up click on Yuna's abdomen (belly) area.

You need to talk to Yuna to receive a quest from her. To do that, catch her during the night in the living room, select "gift" and click on the "talk" option.

Yuna will, essentially, ask you to get running shoes for her. 
Running shoes can be obtained on the night market.
To get to the night market go for a run at night in the first area.

As far as I know you cannot.

Holy hell. Just tried it and it works.

I was convinced that was a WIP feature.

To put the clothes back on, simply click on the ones which have been discarded on and around the bed.

Yuna's shirt is placed into the chest of drawers next to her bed, for some reason.

What are you doing to your game? Once a new build come out simply override the old files with the new ones. I've been doing that since I got the game and my saves always remained.

From what I understand, body levels reduce the wakefulness rise when interacted with.

You need to unlock the tongue by purchasing the 10000 Pcoin upgrade from the store. Once you do, select the tongue, mouse over the desired part and get to licking.

If the licking prompt does not appear move Yuna around until you find what you're looking for.

The game has two currencies: Peeptube coins and credits.

You might've had enough peeptube coins and not enough credits.
You can imagine Peeptube coins as REC's universe cryptocurrency.
Can't really pay your rent with crypto.

Not anytime soon. There was a relatively recent devlog which promised combat sex during the run but that won't happen anytime soon.

You simply press on the clothing which are scattered next to her bed.

Undress Yuna fully, flip her over, move her legs so she gets into the doggy position, start clapping them cheeks, use the hand option to grab her arms to switch to the wheelbarrow animation.

To flip Yuna around you have to first raise both of her arms up and click on her stomach to flip her over.

Part time job pays well but it's mind-numbingly boring.

Godspeed, you magnificent bastard.

Go for a run (during the day). Multiple runs may be required before the cutscene for part time work triggers.

Buy upgrades, use items which reduce wakefulness and work on Yuna's body "skills" by interacting with them during the night.

Check the "body experience" tab in the "stats" tab to see how well Yuna's body is developed.

Click the note next to the cash register. The note lists all of the coin denominations.

If you're lazy, all of the coins are (from left to right):
0.01 -> 0.05 -> 0.10 -> 0.25 -> 1.

[Suggestion/Request]: I would like to request a skylight to be added to the store minigame.
Right now, there's a lot of downtime but if there was a skylight we'd have an entire night sky to look up at while we wait for the customers to show up.

Yuna begins to lock her room at night if your suspicion meter gets too high.

Which is an oversight because in the event where Yuna asks you to unlock her door you lockpick it in record time with the implication being that Yuna locks her room every night.

Once you undress Yuna her clothes are placed either on the bed, on the drawer to the left of the bed or inside the drawer, for some reason.

When you click on the discarded items you can put them back on.
Same with the sheets.

Peak human error right there. 

Define "can't do anything". 
Yuna may not be in her room on some days.

If you mean you load into the night, perform one or two actions and immediately get ejected out then you have no stamina for the night sequence.

Personally, I don't bother with night sequences until I can get around 300 total stamina (from running) and bought the "comfy sheets" upgrade.

Once it becomes night, you need to talk to Yuna, click on "gift" and select the "talk" option. Yuna will reveal that she wants to start running but doesn't have running shoes, giving you your new objective.

No you do not. Going for a regular run will trigger the store cutscene.
It might take a few runs for the event to happen but it will happen eventually.

You do not need to start a new game. I got the shop unlocked on an existing save. Several runs might be required to unlock it.

You have to click on the timer in order to stop time. The one in the top-left corner of the screen which appears during night sequences with Yuna.

The store minigame is having some issues. It should be addressed in a hotfix soon.

Skill issue. Just tested it on the newest version. To open Kaede's sleeping bag you have to click on the zipper, which is located on the very edge of the bottom right corner.

TO unlock the minigame go for a run and start from the beginning. You'll eventually find it.

If we're talking about completing the minigame it is currently bugged.
My advice is to wait until the game updates before you try playing again.

Go to the "Development log", click "view all posts", press ctrl+f, type in "cheat" and search the page.

The full cheat list can be found in one of the earlier dev logs. You'll have to dig a little to find them.

Every time you win a fight you rob someone. Every time you lose a fight you get robbed. Simple as.
Watch your stamina and utilize the "escape" option during fight to avoid losing money. The early game is pretty brutal.