This seems to be a commonly misunderstood thing so I'll do my best to shed some light on it. Keep in mind the following however:
The purpose of this guide is to define some key terms that are often misused, and explain how threads and hyper-threading works in the context of "Set Affinity" in task manager. Which checkboxes mean what, how to use it, why it does things, etc.
Explaining how a CPU works is not the point of this guide; This information is just provided as background to
I'm going to admit to skimming through most of this thread (I did read a bit of the OP), but I feel like either the subject was not explained thoroughly enough or there is some misinformation still being spread about.
A background on processors
To understand how HyperThreading and even Cluster Multithreading (both are similar to an extent), a basic understanding of processors is needed.
A processor is divided up into three major sections
The front end, or contr