Atomic transforms collections of personal Markdown notes into an AI-augmented knowledge graph by breaking documents down into semantically linked conceptual units. Users capture thoughts, research excerpts, and web clippings as modular notes that the system automatically chunks, embeds, and categorizes with hierarchical tags. An interactive force-directed canvas maps out the entire knowledge base, positioning related ideas closer together based on embedding cosine similarity rather than manual folder hierarchies. Built-in vector search queries across text embeddings directly within SQLite, retrieving precise contextual snippets in response to natural language prompts. The automated wiki engine synthesizes disparate notes into comprehensive reference articles equipped with verifiable inline citations back to original source materials. Integrated conversational agents leverage retrieved knowledge context to answer research questions, surface contradictions across past entries, and draft structured daily briefings. External AI tools can read, search, and update stored knowledge through an embedded Model Context Protocol server endpoint. Running on a dedicated VPS on RepoCloud with guaranteed CPU, RAM, and SSD, full root SSH access, and a browser serial console. MIT licensed.