[carapace]

Have you read "Introduction to Cybernetics" by Ashby?

(PDF available here: http://pespmc1.vub.ac.be/ASHBBOOK.html )

Cybernetics might be the "missing link" for what you're talking about.

[crimsonalucard]

I didn't dive to deep into this so I could be wrong but this looks like control theory with elements of category theory.

I'm looking more for a theory of modules and relationships. Something that can formalize the ways we organize code.

[carapace]

From my POV control theory is rediscovering cybernetics, but yeah.

It sounds like CT is what you're after (to the extent that we have it at all yet...)