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The save system is split across a number of solutions and thus can be a little complicated. It may be a candidate for refactoring, but for now it is what it is. The systems involved are:
Assets/_Rogue Wave/Runtime/Roguelite/RogueLitePersistentData.cs: Load/Save managed by Assets/_Rogue Wave/Runtime/Roguelite/RogueLiteManager.cs (see LoadProfile and SaveProfile. Handles all the roguelite progress data for a player profile. Doesn't serialize Unity object references or non-serializable types (e.g. Dictionary).