I like @karpathy's Obsidian setup as a way to mitigate contamination risks. Keep your personal vault clean and create a messy vault for your agents. I prefer my personal Obsidian vault to be high signal:noise, and for all the content to have known origins. Keeping a separation between your personally-created artifacts and agent-created artifacts prevents contaminating your primary vault with ideas you can't source. If you let the two mix too much it will likely make Obsidian harder to use as a representation of *your* thoughts. Search, bases, quick switcher, backlinks, graph, etc, will no longer be scoped to your knowledge. Only once your agent-facing workflow produces useful artifacts would I bring those into the primary vault.