It’s cool that you used your programming skills to aid you! I wonder how much code you had to write to solve it, which libraries were used, etc.
Well, it is possible to solve the puzzles by hand. A “terminal” panel gets upgraded as the story levels are cleared. It gives the player hints about the level that should help in manual hacking. It might require a text document for some levels with ambiguity (there are only a few) so you can track multiple branches.
The game was created for a game jam (although a long and chill-paced one), so the game lacks the polish. The difficulty curve is also all over the place.