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Most of the core library's types lives long-term while emulating so the garbage collector doesn't need to do a whole lot other than marking stuff gen 1 or 2. There may be change for some allocation optimizations by introducing structs though.

Most of the timing issues I had were rather related to the clock sync between the memory, CPU and PPU. For example, I didn't take into account that the CPU doesn't immediately fetch, decode and process an instruction: each step in the process happens on another clock tick.

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