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Tom, I think your interpretation of the second rule is the problem.
We can start by thinking the "end goal of these rules" is for easy of review an sane commit history. Rule 2 states that you should clean up your intermediary history while you were developing. In other words, there's no point in submit lots of changes in the first commits that later is reverted by subsequent commits. This is not the case in this PR: changes are ordered logically, much in agreement with the first rule.
Additionally the second rule does *not* mean you should squash every thing into one commit per directory. Alas one commit per directory is the absolute minimum you are required to (unless the commit falls in the simple search and replace or very trivial changes, in which we have the convention to use the "Global:" prefix in the commit). if you go beyond that and split in logical pieces for easy of review, git history, "revertability", etc , it's even better. Btw if you were only aiming to split into one commit per directory you wouldn't even need to split as the script in gittools directory could do that automatically.
So, defending myself, I don't think it really breaks any rule.
Lucas De Marchi
I did not mean to use your PR as an attack, just an example because it crossed the lines and speaker nicely to both rules. No offense was meant.