You are noting that the logical atomism in the Tractatus reminds us of a large software system, which it does. The problem is that logical atomism isn't actual

You are noting that the logical atomism in the Tractatus reminds us of a large software system, which it does. The problem is that logical atomism isn't actually tenable, as many (not least W himself) have pointed out. But you've actually read the Tractatus and PI, so I'm surprised to hear you still supporting the Tractatus. A full discussion of why logical atomism is wrong is, of course, out of scope here, but essentially, the problem is that there are no logical atoms. As inspiration for programmers, the Tractatus is probably fine. But as the only take on philosophy of language/epistemology that a person might ever read, it is at least very far from where modern thinking is at.