RELEASE: Finalize Semantic Restructuring v0.1.0

- Folders: literate->harness, src->library, system->environment, scripts->interfaces.
- Synchronized all :tangle paths and system definitions.
- Hardened .gitignore for binary and log artifacts.
- Consolidated all documentation into docs/.

docs/USER_MANUAL.org

@@ -0,0 +1,51 @@
+#+TITLE: OpenCortex User Manual
+#+AUTHOR: OpenCortex Contributors
+#+STARTUP: content
+#+FILETAGS: :docs:manual:
+
+* Introduction
+Welcome to OpenCortex v0.1.0 (The Autonomous Foundation). OpenCortex is a neurosymbolic AI agent and a Lisp Machine operating system designed to autonomously maintain your Memex (knowledge base) and interact with you via multiple, equal-citizen interfaces.
+
+* Quick Start Installation
+OpenCortex can be installed and booted with a single command:
+
+#+begin_src bash
+curl -sSL https://raw.githubusercontent.com/gharbeia/opencortex/main/opencortex.sh | bash -s -- setup
+#+end_src
+
+This command will:
+1. Bootstrap the OpenCortex repository into \`~/.opencortex\`.
+2. Install system dependencies (SBCL, Quicklisp, etc.).
+3. Interactively guide you through the initial configuration.
+4. Tangle the literate source code.
+5. Awaken the background daemon.
+
+* Configuration
+The system is configured via a \`.env\` file in the project root. Key variables include:
+
+- \`LLM_API_KEY\`: Your provider key (e.g., \`OPENROUTER_API_KEY\`, \`OPENAI_API_KEY\`).
+- \`PROVIDER_CASCADE\`: The fallback order for LLM providers (e.g., \`openrouter,ollama,anthropic\`).
+- \`MEMEX_DIR\`: The absolute path to your knowledge base (defaults to \`~/memex\`).
+
+* Interacting with OpenCortex
+Once the daemon is running, you can connect via any supported client.
+
+** Terminal User Interface (TUI)
+For a rich terminal experience with history and background worker status:
+#+begin_src bash
+opencortex tui
+#+end_src
+
+** Command Line Interface (CLI)
+For raw, pipe-friendly interaction:
+#+begin_src bash
+opencortex cli
+#+end_src
+
+* The Memex Structure
+OpenCortex manages a local folder structure representing your "Memex".
+- *Nodes:* Every Org-mode headline is a "node" in the agent's memory graph.
+- *Source of Truth:* Plaintext files are the definitive state.
+- *Autonomous Workers:*
+  - The \`Scribe\` distills chronological logs into structured Zettelkasten notes.
+  - The \`Gardener\` repairs links and flags orphaned nodes.