Hey there! Unfortunately there's no save system implemented. I figured most people only play my games once in a single sitting (and honestly I find a them a bit daunting to add). No one's ever asked me to mod a game, but I don't see any problems, so by all means add one for your mod! Obviously just be careful if there's any personal metadata in the files.
It's been a while since I made Ochre, but from what I remember about the code architecture to help you out, important variables for progression are found in the discovered bool for each Location and in the Narrative.cs script.
If spoilers are a concern of yours, be careful because you'll see I hard coded the dialogue (i was a bit messy but it's mostly in Scripts>Locations, but also GoodEnding.cs). Other places to mention would be spoilers in the Sprites folder, and the GoodEnding scene. If spoilers are of no concern to you, go crazy! There's heaps of hidden stuff.