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Will the new version of the 5121e have cache coherency?
From what I've learnt recently, cache coherency is not a big issue itself. Many CPUs don't have it. You can write programs anyway, in this case, kernels.
It merely complicates things if you want to make a kernel that runs on a variety of CPUs, and some have cache coherency while others don't. You would actually need different kernels.
The answer is no, the 5121E (and 5123) are not designed with cache coherency in mind. It is, as you said, a software problem for the most part. The software simply has to make special effort to get the best performance. Of course in certain scenarios cache coherency can make systems slower - snoops and acks and cache management take up valuable system resources. Usually chips built this way don't have too many peripherals though.
We took exception with the 5121E because it has a LOT of peripherals and many of them are driven by a high-speed DMA controller. This will make development a little more hassle than it could have been (and than anyone is used to on PowerPC) but, it is all in a day's work.
At the end of the day, the userspace programs - anything you install outside the kernel, will be exactly the same, so it doesn't affect you guys much.