I'm pretty sure he means exactly that. A programmery "theory" about the subject is something that goes beyond blindly following documentation or rules. It is something that is taught (or self-taught) over time, rather than executed by following instructions.
The author even spent a whole section "Ryle's Notion of Theory" in the article to described precisely what he means by "theory". (More exactly, he describes Ryle's definition, which he is borrowing.)