REFAC: Standardize on Cognitive Cycle and harden harness

USER_MANUAL.md

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+# OpenCortex v0.1.0 User Manual
+
+OpenCortex is a neurosymbolic AI agent designed for autonomous Memex maintenance. It combines the probabilistic power of Large Language Models with the deterministic safety of Common Lisp and the structured clarity of Org-mode.
+
+## 1. Quick Start
+
+Install and boot OpenCortex with a single command:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/gharbeia/opencortex/main/opencortex.sh | bash
+```
+
+Once installed, simply run `opencortex` to start the interactive CLI.
+
+## 2. The Core MVP Skills
+
+The v0.1.0 release includes the following essential skills:
+
+### Safety & Integrity
+*   **System Policy:** Enforces core invariants (Sovereignty, Transparency).
+*   **The Bouncer:** Inspects all proposed actions and blocks high-risk operations.
+*   **Protocol Validator:** Ensures communication integrity.
+
+### Cognitive Kernel
+*   **LLM Gateway:** Routes requests to your preferred provider (Gemini, Anthropic, etc.).
+*   **Peripheral Vision:** Manages context and retrieves relevant notes via Sparse Trees.
+*   **Memory Steward:** Maintains the live graph of your Org-mode Memex.
+*   **Credentials Vault:** Securely stores your API keys.
+
+### Interaction & Actuation
+*   **CLI Gateway:** The primary interface for chatting with your agent.
+*   **Shell Actuator:** Allows the agent to perform safe system side-effects.
+
+### Autonomous Services
+*   **The Scribe:** Automatically distills your daily chronological logs into structured notes.
+*   **The Gardener:** Proactively repairs broken links and flags orphaned nodes.
+
+## 3. Basic Usage
+
+### Chatting
+Type natural language messages into the CLI. The agent will perceive your intent, consult its Memory, and propose actions.
+
+### Memex Maintenance
+OpenCortex monitors your `daily/` directory. Use the Scribe to distill your thoughts:
+`User: Distill my notes from yesterday.`
+
+### Safety Approvals
+When the Bouncer intercepts a high-impact action, it will create a "Flight Plan" in your Memex. You must mark it as `APPROVED` before the agent proceeds.
+
+## 4. Configuration
+
+All configuration is stored in the `.env` file in your installation directory. You can update your API keys, change your Assistant's name, or modify the mandatory skill list there.
+
+---
+*OpenCortex: The Conductor of your Life Stack.*