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/CHANGELOG.org

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+#+TITLE: Changelog
+#+STARTUP: content
+
+* v0.1.0 - The Autonomous Foundation (2026-04-20)
+This is the initial MVP release of the ~opencortex~. It establishes a secure, auditable Lisp kernel for a personal operating system.
+
+** Features
+- **Unified Envelope Architecture:** Actuator-agnostic protocol that decouples routing metadata from cognitive payloads, ensuring all clients (TUI, Emacs, CLI, Matrix) are treated as equal citizens.
+- **Metabolic Pipeline:** Robust Perceive-Reason-Act loop with selective memory rollbacks and graceful shutdown handling.
+- **Verification Lock:** Mandatory skill enforcement via environment configuration. System halts if security policies or bouncers fail to load.
+- **Foveal-Peripheral Context:** High-resolution focus on active tasks with low-resolution skeletal awareness of the rest of the Memex.
+- **The Bouncer:** Last-mile deterministic security gate with Deep Packet Inspection for secrets and network exfiltration.
+- **Autonomous Scribe:** Background distillation worker that turns daily journal entries into evergreen Zettelkasten notes. Verified to distill atomic concepts autonomously.
+- **Autonomous Gardener:** Heartbeat-driven worker that repairs broken links and identifies orphaned nodes in the Memex graph.
+- **Unified Onboarding:** Single-command installation (~opencortex.sh~) with Docker support, OS detection, and automated dependency resolution.
+- **Channel-Aware TUI:** Interactive Croatoan-based terminal client with clean, human-readable formatting for tool results and system logs.
+- **CLI Gateway:** Local TCP socket server for pipe-friendly interaction and frictionless first contact.
+
+** Licensing & Community
+- **AGPLv3 License:** OpenCortex is now officially licensed under the GNU Affero General Public License v3.0.
+- **Contributor License Agreement:** Implemented a broad CLA (~CLA.org~) for long-term project sustainability.
+
+** Architectural Shift
+- Transitioned to **Literate Granularity**: Every function and invariant is now formally documented in its own Org block.
+- **Provider Agnosticism:** Implemented a dynamic LLM cascade (OpenRouter, Ollama, etc.) removing all hardcoded backend dependencies.
+- **Thin Harness Philosophy:** Decoupled the kernel from specific editors or third-party gateways.

docs/CLA.org

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+#+TITLE: OpenCortex Contributor License Agreement (CLA)
+#+STARTUP: content
+
+* Overview
+This Contributor License Agreement ("Agreement") clarifies the intellectual property license granted with Contributions from any person or entity to the OpenCortex project. 
+
+* 1. Definitions
+- *"You"* (or *"Your"*) means the copyright owner or legal entity authorized by the copyright owner that is making this Agreement with the Project Lead (Amr Gharbeia).
+- *"Contribution"* means any original work of authorship, including any modifications or additions to an existing work, that is intentionally submitted by You to the Project Lead for inclusion in the Work.
+
+* 2. Grant of Copyright License
+Subject to the terms and conditions of this Agreement, You hereby grant to the Project Lead and to recipients of software distributed by the Project Lead a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare derivative works of, publicly display, publicly perform, sublicense, and distribute Your Contributions and such derivative works.
+
+* 3. Grant of Patent License
+Subject to the terms and conditions of this Agreement, You hereby grant to the Project Lead and to recipients of software distributed by the Project Lead a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work.
+
+* 4. You Represent That You Are Legally Entitled to Grant the Above License
+You represent that each of Your Contributions is Your original creation. You represent that Your Contribution submissions include complete details of any third-party license or other restriction of which You are personally aware and which are associated with any part of Your Contributions.
+
+* 5. Your Rights
+You retain all right, title, and interest in and to Your Contributions. This agreement simply grants the Project Lead the necessary rights to distribute the project (including under the AGPLv3 or any future commercial licenses).
+
+* 6. Agreement
+By submitting a Pull Request or patch to the OpenCortex repository, You explicitly agree to the terms of this Contributor License Agreement.

docs/CONTRIBUTING.org

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+#+TITLE: Contributing to OpenCortex
+#+AUTHOR: OpenCortex Contributors
+#+STARTUP: content
+#+FILETAGS: :docs:contributing:
+
+* Philosophy
+OpenCortex is built on a "Zero-Bloat" mandate. The core kernel is mathematically pure, pushing all peripheral logic, API integrations, and routing to hot-reloadable "Skills".
+
+* Literate Granularity
+We strictly adhere to Literate Programming using Org-mode.
+- *Never* edit `.lisp` files in `src/` directly.
+- Modify the corresponding `.org` files in the `literate/` or `skills/` directories.
+- Run `org-babel-tangle` to generate the source code.
+- Every architectural decision, constraint, and implementation detail must be documented alongside the code in the `.org` file.
+
+* Skill Creation Standard
+Skills are the building blocks of OpenCortex. They reside in the `skills/` directory.
+
+A skill must define:
+1. *Trigger*: A lambda determining if the skill should activate based on the context.
+2. *Probabilistic Gate*: Optional. Generates a prompt for the LLM.
+3. *Deterministic Gate*: A hardcoded Lisp function that guarantees safety or executes side-effects (the "Bouncer" pattern).
+
+Example Registration:
+#+begin_src lisp
+(defskill :skill-example
+  :priority 100
+  :trigger (lambda (ctx) ...)
+  :probabilistic nil
+  :deterministic (lambda (action ctx) ...))
+#+end_src
+
+* The Unified Envelope (Communication Protocol)
+All inter-process communication occurs via the Unified Envelope. 
+- Always use semantic types: `:REQUEST`, `:EVENT`, `:RESPONSE`, `:STATUS`, `:LOG`.
+- Include routing metadata in the `:META` block (e.g., `(:SOURCE :TUI)`).
+- Ensure generated `:REQUEST` messages include a mandatory `:TARGET` field.
+
+* Pull Request Process
+1. Ensure your working tree is clean.
+2. Write tests for your skill in `tests/`.
+3. Tangle all files.
+4. Run the test suite: `sbcl --eval "(asdf:test-system :opencortex)"`.
+5. Submit a PR outlining the architectural intent and the specific Literate changes.

docs/USER_MANUAL.org

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+#+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.