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 Well, qemu can do this. Qemu and gdb will let get pretty close. But, I'm sure you are aware of qemu. 

The issue is for hardware integration you have to write the qemu drivers.

Now, in HDL you can do this exactly. You can simulate every clock cycle exactly as you say. Vivado can do this.

It can do this quite well for a microblaze or small riscv. But it would be intense for anything more complex. 
 Vivado brings back pure nightmares XD
Man I haven't used it since senior year, then my edu license expired and I was like yeah I'm good. I very lightly dabbled with the Lattice tools and realized they had far better UX 

> Well, qemu can do this. Qemu and gdb will let get pretty close. But, I'm sure you are aware of qemu. 
Have heard, but never done!  
 Maybe Ghidra too?? Haven't played with that in a while either.  
 Ghidra is good for reverse engineering, not so much forward.

Oh ok, yeah I think you'd like qemu and gdb. For supported microcontroller (popular ones) even the hardware is modeled nicely. Assembly writing and debugging is not a problem.

The issue is, if you chip is supported in qemu.