In the Matrix, what happened after the humans and the robots formed a truce?

There are no further in-universe works. What lays before humanity and their robot overlords remains a mystery.

I am not aware of anything else in production, and I would frankly be surprised if any further works were made. I believe the financial backers found the response to the 2nd and 3rd movies underwhelming.

Same thing that happened the previous seven times.

Sarcasm aside, if you can find a transcript of the Neo/Architect conversation in Reloaded, sit down with a dictionary and thesaurus and decode what the Architect says. It's been years since I saw the conversation, but he speaks in an insanely precise manner, as if to leave no ambiguity, which makes him hard to understand.

Basically, to paraphrase BattleStar Gallactica, all of it happened before and all of it will happen again. The only variation is that Zion survived this time. At the End of Revolutions, the Architect and the Oracle are talking in a rebuilt and reset Matrix.

The long and short is that there won't be peace, in the sense that everyone are friends now, and it could just lead to the waltz between man and machine continuing on, going for a ninth iteration. But, we'll never know, the MMO could be argued as non-canon, but nothing else comes after Revolutions, so take it as you will.

I've always felt that the final animated short in the Animatrix took place after the deal, where humans seem to have at least the possibility of a quasi existence on the surface and try to "reason" with the machines.

The impression I got was that there was sort of tacit approval of this from the Machine City, since they could certainly just send in the "bombers" and blow up any human-made lab on the surface. Those machines have a form of free will, it seems, just like the sentient software programs which are, per the deal if I understood it right, now allowed to come and go between the Machine City and the Matrix at will.

I've long believed that much of The Matrix Trilogy is about reading between the lines. My interpretation is that the machines won. All throughout the movies there is talk of how 'choice' is the issue with the matrix, and how this 'choice' is the flaw in an otherwise inherently perfect system. The idea of course, is that the machines want humans to 'choose' the matrix, that's how they would win right? Well, there is considerable evidence supporting that the humans did just that.

So how does this work? There is a confirmed Matrix, a virtual reality environmentprison for humans, and a supposed real world. Well, since everyone is in the Matrix to begin with how do we know for sure anything is real? Physics. In the real world you cannot bend rules, the laws of science strictly shackle you to normalcy. In the beginning we can see clear definition on what is the Matrix, and what is not. However, during the latter end of the movies we see that Neo's powers extend into the real world. This is impossible, flat out, period, introducing doubt that real world is in fact 'real'. (I'll come back to this)

Secondly we know from Neo's conversation with the Architect that Neo is in fact an anomaly within the Matrix. This suggests that there is some sort of bug that grants Neo his powers. Science, my friends, is why Neo is special. So, if his powers are sourced from some un-fixable bug within the Matrix, the only way for them to work outside the Matrix... is if he is still within the Matrix... (plot twist!)

The first Matrix was perfect, no war, utopia as we are told, and it failed because humans needed choice. Hence the war. This is hinted, flat out communicated, innuendoed, you name it, it's driven in the movies all over the dam place. However, never not once did the machinesprograms mention anything about humans refusing the program entirely or otherwise escaping their shackles, only that there was a mental rebellion to the host program.

Neo displays amazing abilities, but he is not the only entity that displays such skills, programs all over the place in the Matrix also show that they have abilities, this suggests that Neo is in fact a program.

Let's recap: There must be choice, Neo isn't unique, Neo's abilities extend beyond what the characters feel is the Matrix, Zion has been wiped many times in a cyclic run of what seems to be a war about choice, it has been clearly stated multiple times there has been multiple Matrixs (Matrices), and there are a crapload of machinesprograms with strange double-agent objectives to the point that nobody has any idea what side anybody is on.

To conclude...

TL:DR ::There was no real war. Nobody ever made it out of the Matrix. Neo was an unaware program designed to help the humans choose the SECOND Matrix. The 'War' was actually the humans fighting the OS of the FIRST Matrix.

Assuming that Zion doesn't lie within a subsequent matrix, the machines will likely release all those that refuse the matrix as it stands allowing them to join Zion, just as the architect said to the oracle, and being that the machines will exist indefinitely they can allow the humans to live until all of their resources are inevitably expended, which is only hastened by the number of those that the architect releases from the matrix, and those that exist outside of the matrix die. However there are those that will still accept the matrix and the machines will continue on long after all of the humans outside of the matrix have died off so the matrix continues on, the machines do their best not to let another smith esque program overrun the matrix, and in turn things go back to the way they were before the events of the matrix.