Thanks for clearing that up- do you think there would be many ELF executables written whereas linux isn’t as popular an os? I can patch my windows system, but not sure if linux will have a patch as well? Or is it just dependent on patchign the intel stuff and linux will then be protected somewhat too?
Patching is a somewhat different issue. I don't know how things will be patched but I do know that it won't require patching every EXE and ELF. That's because non-malicious EXEs and ELFs are not a problem. I think the patching will be in the kernel, but I'm not sure how you stop the potentially malicious behavior. One possibility may be to not patch anything but to add another layer of behavior-based defense. That would be a relatively simple monitoring program (probably added to the kernel) that would monitor for particular bad behavior by user mode EXEs or ELFs. The reason why behavior-based defense may be possible is that side channel attacks exhibit very distinct repetitive behavior they must repeat millions of times to execute an attack.
Then the first job of an attacking program would be to try to kill the monitor. But that's an arms race that is familiar to antivirus people. Perhaps antivirus vendors will add the capability, or perhaps the OS vendors or open source Linux kernel people will have to do it. Ultimately the chip vendors will have to fix it.