This guide will be updated whenever there's a major update to the game/strategies (e.g new levels, new routes found, updates to existing maps that render's current route obsolete). If you have any feedback or better routes do feel free to comment them down below, I'll try them out. [routes were made as fool-proof and as little technical aspect as possible]

All stages will be done within the same save file, which means that augments are brought over from previous levels (important).

Start by walking forward to climb the chains then jump onto the pipes, and proceed to open the door and speak to Filemon (be careful when walking on the railings, there's an invisible barrier on its side that may push you down).
Select the Thermoptic Camo (Invisibility) Augment and choose whichever weapon you like (does not matter for this route). Go down the stairs to the right which there will be a door on the left, then down the stairs until you see an entrance on the right
Run through the corridor and there will be a console that unlocks the door with the code 'polska'. Enter the first room on the right and talk to the commander about Filemon, which then you can exit the level by the train on the tracks

This level can be done as a pacifist
Head past the civilian and up the stairs. Once you're outside, head straight towards the Mall (be careful not to get hit in the crossfire). Use the invisible augment when trespassing into the Mall, head left and down to take the lift
When you reach the 3rd floor, go invisible and head straight while keeping right. Follow the path on the rooftops and there will be a long pipe leading to another roof top, pick up the blackmail there and head to the bar. The quickest way is to scale down the building off the ledges, which brings you very close to the bar
Talk to the Polish Commander in the bar to trigger his quest dialogue, and talk to him again to handover the blackmail. You can now head back to the train and end the level

Go behind the train onto the platform, there will be a lift to take you down to the ground floor.
Don't forget to give the girl a head pat on the way
Once on the ground floor, go onto the main road. There will be 4 T-55 tanks that you need to destroy. You can use the Sabre and slowly destroy the tanks (slightly safer), or jump on them and use the code 'password' on their consoles. You can also use the camo augment to de-aggro the tanks before they start shooting. After destroying the tanks, you can head back to the train and end the level.

Someone has already made a detailed walkthrough for Belgrade,
I'll be using the ending in their speedrun strategy in my route
https://steamproxy-script.pipiskins.com/sharedfiles/filedetails/?id=3435711108
At the start, head right and get into the building. Walk towards the center onto the corpse and it will open up a hidden stairway.
Head down the stairway and pick up the school keycard in the first locker of the room on the right. Then you'll need to head to the other room and activate the lift. In the lift lobby you can grab a Makarov that's held by a dangling arm.
Head down the ladder and go further down to the school facility, below will be a top-down map of the school facility.
When you enter the school facility, go straight and hug the right wall until you reach the (1)connecting hallway. You can shoot the glass on the left and access the (2)monster observatory. Behind the glass panels in the observatory, there's a console that you can use to open the locked doors with the code 'password'. You can then shoot the red thing in the locked room and head to the (3)ventilation shaft to ride it to the end.
https://www.youtube.com/watch?v=sN9YmQrmEgM

Run towards the Musika Automata building and kill the civilian guarding the building's entrance. Then you can enter the building to take the stairs and head to the second level to enter the nightclub, or you can jump on the scaffolding to the left directly to the nightclub's entrance. You'll need to jump past the club guard by jumping then crouching while moving forward at the corner of the entrance to sneak in, then kill the patron with the cigablunt and take it (extremely important for health and stamina unless you want to spend more time in the wasteland). After killing the patron, be prepared to exit the nightclub ASAP as all nightclub guards will be firing at you.
https://youtu.be/VP5Eycn2Dkg
Once you're outside, continue the path along the pipes leading into the wasteland until you reach the train tracks at the end. Then continue onto the train tracks towards the left until you reach the PSR checkpoint.

Arriving at the checkpoint, you will need to kill Captain Tomasz and the Civilian at the counter and proceed into the path leading down to Tomasz's Office. Go outside towards the left of the office to climb into the second floor, that's where you'll see the Rail Line computer which you can interact with and it brings you to the ending.

To get into the second floor, you'll need to charge up the sabre with secondary fire(default mouse2/ right mouse button) and stick it into the wall at a relatively precise height and angle; follow the lineup in the video below, jump with the mobility augment activated and slightly move backwards at the top of the jump and pierce the sabre into the wall (yes this is very technical and unfortunately this is the only way I know of currently). You can interact with the giant monitors and it brings you to the ending.
https://youtu.be/Q5ccQnuTadE