Hm, if so, then does Hypnospace Outlaw also count? That game has a lot of secrets and special programs that let you find hidden/unique stuff, and it's used to find crucial things in the final chapter, but most of them are already available right from the beginning if you know where to look, and the game is designed in a way where finding those early on is intentional for second-time players (either because it helps skip some chapters, or gives you useful upgrades sooner than you'd normally find them).