Were all US soldiers in the Revolutionary War war criminals? What about the North in the Civil War? Or WWI/WWII?

Nearly every soldier in any war will have directly or indirectly killed an innocent civilian. Which ones are war crimes and which aren’t?

How do you decide and who gives you the authority to do so?

I'd say anyone who chooses to kill a civilian, whether based on an order or not, is a war criminal. I really don't care if they thought they were there for a noble cause or not.

What if they choose to kill a person who was a civilian until they were drafted into the enemy army the day before?

What if the civilian they kill has a substantial effect on the enemy's military capabilities, for example by being someone famous who loudly endorses the honour of signing up to fight for one's country, thereby motivating thousands of young men to do just that?

What if killing a soldier’s children might make him lose his resolve or act erratically? What if destroying an entire city full of millions of civilians might make the enemy lose hope and surrender? What if poisoning the land and water for decades could prevent the enemy from reconstituting itself? What if killing all the women could prevent the production of future soldiers?

Once you open the door, where do you draw the line?

What does indirectly killed mean?

Sounds like a weird way to phrase collateral damage?

Collateral murder.

Civilians die in wars, and that's with the best intentions of all parties to the conflict. If one or both has got radicalised, then a lot of civilians die in war.

you are justifying 9/11 attack on the US, the similar logic to yours was used by Al-Qaeda

No, I'm explaining to you that accidental civilian casualties in a war is a normal part of the terrible activity that is war. Good soldiers with the best of intentions will kill civilians in a war, because war is chaotic and very dangerous.

Radicalised soldiers and armies will give less and less concern to civilians, and at a certain hated level civilians actually will get targeted by individual soldiers or squads. If it then moves up the command chain and there's not enough accountability or pushback from the top leadership then you get to proper genocidal actions like what happened at Srebrenica.

Targeting civilians for death is not acceptable or justifiable.

This is the Israeli take that is continually pushed to normalize their approach to "removing baby terrorists"

Who gives US president authority to just murder whoever he wants?

Nobody. He just seized it. No one gave it to him; hence their upset that people like duterte are being kept in the Hague.

US voters

A group which has been known to collectively make a mistake or two

Correct. Either all soldiers are war criminals or none of them are. The world is black or white, without nuance.