*2025-06-04* (Preview) The `cos` command-line tool serves as the primary interface for interacting with [[Cognition OS]] file systems. Built specifically to work with the markdown-first architecture of Cognition OS, this tool provides programmatic access to your cognitive vault, enabling advanced operations that go beyond what traditional markdown editors can offer. At its foundation, `cos` embodies the principles of [[Semantic Referencing]]—it doesn't just retrieve documents, it understands the choreography of thought embedded within them. Where traditional command-line tools treat files as isolated units, `cos` recognizes that in Cognition OS, every markdown file is part of a living network of meaning. The tool parses semantic markers—those asterisks, exclamation points, and tildes that transform dead links into cognitive instructions. When you execute `cos fetch "note-name" --starred`, you're not just grabbing text; you're following a carefully crafted path of understanding, collecting only the concepts marked as essential for comprehension. The beauty of semantic referencing shines through in how `cos` builds context. Rather than dumping everything connected to a topic, it respects the intentionality embedded in each reference. A link marked with an asterisk isn't just related—it's required. A tilde doesn't just connect—it challenges. The tool reads these choreographic cues and assembles context that mirrors how you actually think about these connections. This makes Cognition OS more than a storage system; it becomes a map of understanding itself. Integration with AI systems showcases the power of this approach. When `cos` prepares context for an AI conversation, it's leveraging semantic referencing to create not just relevant context, but _appropriately framed_ context. The tool understands that feeding an AI everything about a topic is less valuable than feeding it the right aspects approached the right way. This is the difference between information retrieval and understanding retrieval. The tool operates directly on the Cognition OS vault structure—a main vault folder for semantic knowledge and daily notes for temporal captures. By maintaining a lightweight index that tracks both content and semantic relationships, `cos` can traverse your thought network at the speed of intuition. Every command, from simple fetches to complex semantic analysis, honors the principle that references should carry meaning, not just addresses. As semantic referencing evolves within your vault, `cos` evolves with it. The tool can analyze how your referencing patterns change over time, identify concepts that have shifted from tentative connections to load-bearing dependencies, and even suggest where semantic markers might clarify the role of existing links. It transforms Cognition OS from a passive repository into an active participant in your cognitive development, making the invisible choreography of understanding visible and computational.