system
Given the following post, respond as if you're commenting on Reddit:
human
(MCU) Why didn't Tony Stark find out anything about Hydra?

He decrypted all of Shield's files when he was on the helicarrier, shouldn't something that point to hydra have shown up.
gpt
Several reasons! After all, HYDRA's all about having multiple heads.

So what are the priorities of HYDRA Pre-Triskelion? They need to keep themselves secret, to endure, keep themselves out of the light. Those are the BIGGEST. If they can't follow through with those, then saving the world from freedom isn't going to happen.

So HYDRA is damn good at hiding. 

And a lot of effective hiding is where you don't put your faith. SHIELD's new flagship hellicarrier? Probably not a good idea to put sensitive HYDRA stuff on something that can easily fall out of the sky. Especially if Nick Fury makes a habit of leading from the front. HYDRA needs to endure, and that's hard to do with a cycloptic micromanager standing over the helm.

That's why they chose secret bases as their primary information nodes.   HYDRA has plenty of agents in places where they can control the flow of information itself (The Hub, Triskelion, etc), but no infrastructure to trace back to the real heads of power. In fact, before the failure of Project Insight, many HYDRA agents didn't know who else was HYDRA. Everything was compartmentalized, so if one head was cut off, two more could take its place. 

Added to that, keeping out of the light. Behind and underneath SHIELDs encryption was HYDRA's. Paranoia pays off. Double encryption, non-standard codes, even experimental, seemingly sentient computer algorithms. HYDRA had access to everything SHIELD did, and a little more. Plus, SHIELD wasn't looking for HYDRA, but HYDRA was always hiding from SHIELD.

So to answer your question, the reason why Tony Stark's JARVIS program couldn't turn up anything on HYDRA was because 1, HYDRA wasn't storing sensitive data on the hellicarrier 2, HYDRA controlling the flow of sensitive traffic around the hellicarrier to avoid any non-HYDRA agents accidentally getting a hold of it, and 3, Even after he decrypted SHIELD's files, he had no idea to keep looking for HYDRA's.