Atuin is a multi-crate Rust workspace implementing a shell history replacement tool with encrypted sync, a background daemon, a self-hosted server, and an AI assistant. The system replaces the default shell history with a SQLite database that records additional context (exit codes, working directories, session IDs, command durations) and provides fast, fuzzy search via a TUI. History is captured through shell hooks (bash, zsh, fish, nushell, xonsh, PowerShell) and optionally via a PTY proxy that captures command output for full-text search. A background daemon (atuin-daemon) manages history journaling, output capture persistence (Fjall blob store + SQLite FTS5 index), AI session capture from coding agents (Claude Code, Codex, opencode, Pi), and encrypted record sync with the server. The server (atuin-server) is an Axum HTTP application supporting SQLite, Postgres, and MySQL backends, providing user authentication, record sync endpoints, and capability negotiation. The AI subsystem (atuin-ai) includes a TUI chat interface, inline command mode, MCP server, skills system, and permissions framework for safe tool execution. Key entry points include the CLI binary (crates/atuin/src/main.rs), daemon boot (crates/atuin-daemon/src/daemon.rs), server launch (crates/atuin-server/src/bin/main.rs), and AI inline command (crates/atuin-ai/src/commands/inline.rs). External dependencies include SQLite, tokio, tonic (gRPC), Axum, serde, paseto, and various shell-specific integrations.