What makes you think she hasn't done this? The point of the article is that "tools for thought" as presented by Ken Iverson and others are a narrow focus in a much broader subject. Since her aim is to zoom out it makes sense to defer mention of Iverson. It's not indicative that she hasn't engaged with or understood his work.
Writing, drawing, and on-paper math are representational media. The process of writing, drawing, or calculating/proving is a form of manual processing because it requires organisation and transformation of representations.
Automated - computed - processing is a completely new category. It's a metaprocess which allows processes themselves to be represented and processed mechanically.
A lot of computing only does this is in a very basic way. The web is essentially a document distribution medium. Note organisers are essentially just a paper substitute that let you draw arrows and move things around, possibly with some hyperlinks.
They're both representations that support manual processing but don't improve on it. So they don't offer metaprocessing for most users. And with current tools metaprocessing is barely an option for most developers.
A genuine automated tool for thought would do the organising and summarising for you, perhaps teaching you if you needed that. But more - it would also improvise its own processes for achieving those ends.
Or at least make it easier for you to improvise your own at an abstract level that would be much higher than conventional code representations.
[1] Using an unaided human brain. Not hands, except incidentally.