Launch the game again, for me it works the second time around.

You can try to validate the game cache by going to your Steam games library, select Hunt Down The Freeman, right click it and go to properties, local files, and then click verify integrity of game files.... Mine needed to redownload a file but I have no idea what it was.

There's a game crash upon loading a level when you're on a bike in a tunnel. Try going into the tunnel without the bike.

There doesn't seem to be a hint for the prone feature, but you can crawl under things using the (z) key.

There's a part with an overturned truck blocking the path ahead. The truck is supposed to get destroyed allowing you to progress, so you might need to noclip to the other side if it doesn't blow up. Various parts of the game have issues where you can't progress without the use of noclip.

Go to the gameplay options and enable the console, then in-game hit the console button (`) and run commands:
sv_cheats 1
noclip

Then close the console and move to where you want to be, and run the noclip command again to move normally. Also you could bind noclip to (v) by using the command:
bind v noclip

Define a key to holster your weapon from the options, then go up to something climbable and press or hold (space) to climb it, and forward (w) to move upwards, and sometimes (space) to jump off.

Try pressing the nightvision key (6) and (left-click) to engage it.

To disengage nightvision, press (6) and (right-click).

(Middle mouse down) is my default button to select the underslung grenade weapon, which fires using (left mouse click).

If (middle mouse down) fails to select the underslung grenade launcher then try (right click) to use the sight for a moment, and then (middle mouse down).

The sub-machine gun and assault rifle are both selected from the (3) key, but only one can be bound to the key at a time. Hold (tab) to find your inventory menu and (left-click) a weapon to set it as the default one.

Start a new game from the closest chapter. HoodlessKenny also suggested: "The bug for the weapon not firing can actually be fixed with the "ent_remove" and "give" commands. For example, if the AR2 stopped working, type "ent_remove weapon_ar2; wait 5; give weapon_ar2". As for why the glitch itself occurs, it always happens after reloading and may involve +attack2 happening at a precise moment before or after the reload key is hit."

Other weapons:
ent_remove weapon_ak47; wait 5; weapon_ak47

Sometimes items auto-pickup when you're close enough, and other times you need to press the use key on them (e).

Unlike Left 4 Dead or PLAYERUNKNOWN'S BATTLEGROUNDS It's possible to hold the painkiller item without actually having painkillers to consume in this game, so the pot is like a weapon and pills are ammunition.

Go to options, gameplay, and put the crosshair on.

I can't find a setting or command to make them permanent, but to see them again briefly press (TAB).

The default setting in my game was 5.1, but I actually use headphones, so check that your audio setting is correct.

If you get sick of the ambient sound then run console command:
stopsound

Try to keep any props out of the way of friendly AI. The game seems to end if they run into a prop.

At one part in a subway tunnel your ally might run backwards towards danger while you need to turn a valve(hidden behind some boxes) to crawl under to the other side and turn another valve to open a gate for your allies.

After going up the elevator, find a cable behind a crate and press the use (e) button on it to bring it into the elevator again. Ride the elevator back down where you'll find an ally, but keep any props out of his way to prevent the HL2_GameOver_Ally bug. Don't forget to take the sniper rifle, then connect the cable to the sockets in the fenced off wall.

Walk your way through the minefield but make sure your path doesn't go too near the mines. Every mine has some space between it and the nearest ones to it, but some gaps are larger than others, so you have to go for the larger gaps. When you reach the green computer with the blue screen simply go up to it and press (e) and then your teammate should run through the mines without them blowing up.

Where several characters are holding off unlimited waves of enemies; there's a valve behind some boxes. Get the boxes out of the way using (e) then turn the valve until it doesn't turn any further, then crawl under the gate using (z) and turn the valve on the other side fully too.

Go up to the roof of the train and jump along towards the rear carriage, eventually a minigun should appear. You can pick it up to defend the train against flying enemies, but the enemies are an infinite wave that you don't seem to need to shoot down. Simply go to back into the driver car and the level should end.

If you set a button to holster weapon and press it, then press (space) against an object like a ledge or pipe, you might be able to climb it.