Perhaps a checkbox before the ship name would make you jump to the commander?

It's a good idea and has been suggested multiple times.

Meanwhile, back to your question:

And how do I know who is commanding what?

You have all the info already, just need to use multiwindowed mode. You know the name of the ships and on the fleet view you are able to see the commander in charge.

Also, in terms of changing, you can just select a more suitable commander and just assign it, which will relieve the current commander of the ship with the one you are selecting.

Don't get me wrong, far from ideal especially when you have thousand commanders to look at, however, what you are trying to do is already possible; time consuming, but possible.

Given by the number of posts that I've seen pop up, both on this forum and on Reddit, over the years; I think it might make sense to have any NPR that's currently marked as Neutral to automatically be set to Hostile when they open fire on your ships or kill a ground unit.

This should help curb at least one of the causes of the common message of "why can't I shoot back?"

I like the principle, but I think there's a lot of annoying "edge" cases where this wouldn't work.

Generally there are plenty of roleplay circumstances where you would want relations to remain nominally neutral after firing or being fired upon, which could range from warning shots fired at a scout or survey ship infringing your territory up to a conflict limited to only one or several systems but not a full-scale galactic war. In this case, automatically setting races to Hostile status can lead to some undesired expansion of the conflict, such as:

• STOs in "non-involved" systems may fire on the now hostile ships.
• Ground forces on shared bodies in non-involved systems will engage each other.
• Mines (of the explosive variety) may trigger unexpectedly.
• Specific to NPRs, but in "warning shot" situations additional unintended fire in other locations, for example from fire controls set to fire at will (e.g., "Oops, there goes the alien diplo ship"), will worsen relations and make it much harder to restore neutrality after firing said warning shots.

Note that shared bodies are particularly relevant in games with multiple player races, but also can be relevant in games with NPRs - particularly in cases with mixed player race and NPR starts in Sol, which is not an uncommon setup.

At the very least, it needs to be a toggled behavior which isn't something we have a lot of in the Aurora UI, and would likely cause just as many issues for the kinds of players who are likely to run into the above scenarios (e.g., NATO vs Soviet, "I shot at their survey ship, why are the Soviets invading Poland?" situations).

With the current behavior or with a new toggle switch, in either case the solution is "RTFM" and, since if we're being honest here the "FM" is not very readable maybe some better or more accessible documentation would be useful. That said, either way, it is a lesson a player learns once and then (usually) remembers for the next time.

P.S. Is this by any chance a suggestion motivated by recent events in the Blue Emu AAR @ Pdox forums? If so, I'd hesitate to draw a lot of conclusions from that experience, as Blue Emu is a great authAAR but really doesn't read the documentation very well and this is far from the first fairly basic error in understanding he's made in that AAR.

Perhaps a checkbox before the ship name would make you jump to the commander?

And how do I know who is commanding what?

What would be the best way to remove these commanders?
The problem is that I find no way to focus the left tree on the commander to remove.