DOCS: Refine roadmap and expand Anatomy. RENAM: Rename Emacs package to opencortex.el. CLEAN: Purge legacy scripts.

CONTRIBUTING.org

@@ -31,7 +31,7 @@ Example Registration:
 #+end_src
 
 * The Unified Envelope (Communication Protocol)
-All inter-process communication occurs via the Unified Envelope. Do not use legacy specific types like `:CHAT`.
+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.

README.org

@@ -43,15 +43,16 @@ The Lisp microkernel is a thin, unbreakable harness strictly responsible for:
 In opencortex, a Skill is simply a *single .org file* containing everything: the documentation, the AI instructions, and the deterministic Lisp code. When the system boots, it compiles these skills directly into the live Lisp image.
 
 ** The Anatomy: Three Data Stores
-1. *The Linguistic Substrate (Plaintext Files):* The human-readable Source of Truth on your hard drive.
+1. *The Linguistic Substrate (The Memex):* A collection of plain-text Org-mode files on your local disk. This is the ultimate Source of Truth. Because it is plaintext, it is human-editable, version-controllable, and platform-independent. In OpenCortex, your notes, tasks, and code aren't just "data"—they are the agent's actual configuration and memory.
-2. *The Lisp Memory (RAM):* The "Active Brain," a live, threaded graph of Lisp objects representing your Memex.
+2. *The Lisp Memory (RAM):* A live, homoiconic graph of Lisp objects. Upon boot, OpenCortex ingests your Memex files and transforms them into a high-performance in-memory graph. 
-3. *The Telemetry Store (External):* A high-volume database for sub-deterministic sensory data.
+   - *Why RAM?* Traditional databases require expensive joins and context-switching to traverse complex associations. By keeping the entire graph in RAM, OpenCortex can perform semantic traversals and logical inferences at native Lisp speeds. 
+   - *Homoiconicity:* Since the program (Lisp) and the data (Lisp objects) share the same structure, the agent can manipulate its own memory as easily as it manipulates its own code.
+3. *The Telemetry Store (External):* A high-volume database for sub-deterministic sensory data (system metrics, sensor logs) that the agent monitors and distills into Org-mode "insights."
 
 ** The Psychology: The 2x2 Cognitive Matrix
-| | Probabilistic (Neural/Intuitive) | Deterministic (Deterministic/Logical) |
+|                      | Probabilistic (Neural/Intuitive)                                           | Deterministic (Deterministic/Logical)                                              |
-| :--- | :--- | :--- |
+| Foreground (Active)  | *The Interface:* Fast AI models for conversation and multimodal ingestion. | *The Steward:* Lisp engine that safely retrieves data and enforces security rules. |
-| Foreground (Active) | *The Interface:* Fast AI models for conversation and multimodal ingestion. | *The Steward:* Lisp engine that safely retrieves data and enforces security rules. |
+| Background (Passive) | *The Editor:* Deep AI models finding patterns while you sleep.             | *The Librarian:* Lisp engine maintaining data integrity and filing notes.          |
-| Background (Passive) | *The Editor:* Deep AI models finding patterns while you sleep. | *The Librarian:* Lisp engine maintaining data integrity and filing notes. |
 
 ** The Physiology: Five Core Processes
 1. *Perception:* Automatically vectorizes your input and sets the "Foreground Focus."
@@ -81,17 +82,26 @@ opencortex cli
 * The Evolutionary Roadmap
 
 ** v0.1.0: The Autonomous Foundation (Current Release)
-The initial MVP establishing a secure, auditable Lisp kernel. Features a robust metabolic pipeline, mandatory skill enforcement, and background distillation.
+The initial MVP establishing a secure, auditable Lisp kernel. Features a robust metabolic pipeline, mandatory skill enforcement, and background distillation (The Scribe).
 
-** v1.0.0: The Verified Wrapper (Current Target)
+** v0.2.0: Interactive Refinement & Self-Editing
+Elevating the user interface and granting the kernel the physical capability to edit its own source code.
+- *Autonomous Self-Editing:* Implementation of File I/O cognitive tools (`:read-file`, `:write-file`, `:replace-string`) and whitelisting `emacs` for autonomous `org-babel-tangle` operations.
+- *High-Fidelity TUI:* Transitioning to a rich, native Lisp TUI via `croatoan` with scrollable history and multi-line input.
+- *Skill Hot-Reloading:* A dedicated mechanism to safely swap compiled Lisp code into the live image without severing client connections.
+- *Automated PATH Handling:* Zero-config installation where the `opencortex` binary is automatically injected into the user's environment.
+
+** v1.0.0: The Verified Wrapper (Next Major Target)
 Achieving feature parity with SOTA autonomous agents but with Lisp-grade mathematical security. 
-- *The Tools are External:* Standard bash shell, headless browser (Playwright), and standard file I/O.
+- *The Tools are External:* Standard bash shell, headless browser (via Playwright), and standard file I/O.
-- *The Safety is Internal:* The Bouncer and Formal Verification gates mathematically prove actions are safe.
+- *The Safety is Internal:* The Bouncer and Formal Verification gates mathematically prove actions are safe before they touch the OS.
 
 ** v2.0.0: The Cannibalization
-Replacing string-based tool wrappers with native Lisp data structures.
+Replacing string-based tool wrappers with native Lisp data structures to eliminate LLM fragility.
-- *Cannibalizing the Browser:* Ingesting the DOM as a native Lisp AST.
+- *Cannibalizing the Browser:* Ingesting the DOM as a native Lisp AST rather than fighting with Playwright scripts.
-- *Cannibalizing the Shell:* Moving from bash execution to native OS API bindings.
+- *Cannibalizing the Shell:* Moving from bash execution to native OS API bindings. Emacs becomes a viewport for the live AST, not a master.
 
 ** v3.0.0: True Symbolic Determinism
 The great inversion. The Lisp engine takes the wheel, and the LLM is relegated to a mere semantic translation layer for the messy outside world.
+- *Deterministic Planning:* The core reasoning engine uses formal logic and graph traversal to plan and execute workflows.
+- *Self-Correcting Syntax:* The Lisp engine catches and repairs hallucinated syntax errors without consulting the LLM.

USER_MANUAL.org

@@ -6,51 +6,46 @@
 * 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.
 
-* Installation
+* Quick Start Installation
-OpenCortex is bootstrapped via a single shell script.
+OpenCortex can be installed and booted with a single command:
 
 #+begin_src bash
-git clone ssh://git@10.10.10.201:2222/amr/opencortex.git
+curl -sSL https://raw.githubusercontent.com/gharbeia/opencortex/main/opencortex.sh | bash -s -- setup
-cd opencortex
-./opencortex.sh setup
 #+end_src
 
-This process will install SBCL, Quicklisp, and prompt you to create a `.env` file for your API keys.
+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. Essential variables include:
+The system is configured via a \`.env\` file in the project root. Key variables include:
 
-- `OPENROUTER_API_KEY`: Your LLM provider key.
+- \`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`).
+- \`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`).
+- \`MEMEX_DIR\`: The absolute path to your knowledge base (defaults to \`~/memex\`).
 
 * Interacting with OpenCortex
-Because of the Unified Envelope Architecture, the kernel treats all clients as interchangeable. You must first boot the background daemon:
+Once the daemon is running, you can connect via any supported client.
-
-#+begin_src bash
-./opencortex.sh --boot &
-#+end_src
 
 ** Terminal User Interface (TUI)
-For a rich, split-pane terminal experience:
+For a rich terminal experience with history and background worker status:
 #+begin_src bash
-./opencortex.sh tui
+opencortex tui
 #+end_src
 
 ** Command Line Interface (CLI)
 For raw, pipe-friendly interaction:
 #+begin_src bash
-./opencortex.sh cli
+opencortex cli
 #+end_src
 
-** Emacs Integration
-OpenCortex functions as your "foveal vision" inside Emacs.
-1. Ensure `org-agent.el` is loaded.
-2. Run `M-x opencortex-connect`.
-3. Interact via the `*opencortex-chat*` buffer.
-
 * The Memex Structure
-OpenCortex assumes a local folder structure representing your "Memex".
+OpenCortex manages a local folder structure representing your "Memex".
-- Core memories and identities are mapped to Org-mode files.
+- *Nodes:* Every Org-mode headline is a "node" in the agent's memory graph.
-- The `Scribe` background worker distills chronological logs into structured Zettelkasten notes.
+- *Source of Truth:* Plaintext files are the definitive state.
-- The `Gardener` continuously repairs broken links and flags orphaned nodes.
+- *Autonomous Workers:*
+  - The \`Scribe\` distills chronological logs into structured Zettelkasten notes.
+  - The \`Gardener\` repairs links and flags orphaned nodes.

docs/deployment.org

@@ -1,36 +0,0 @@
-#+TITLE: Deployment Guide: Containerized OpenCortex
-#+AUTHOR: Amr
-#+DATE: [2026-04-11 Sat]
-#+FILETAGS: :deployment:docker:infrastructure:
-
-* Overview
-The ~opencortex~ is designed to run within a Docker container to ensure system dependencies (SBCL, Quicklisp, signal-cli) are perfectly matched across different host environments.
-
-* Prerequisites
-- Docker Engine
-- Docker Compose
-- A valid ~.env~ file in the ~projects/opencortex/~ directory (refer to ~.env.example~).
-
-* Quick Start
-** 1. Build and Start
-From the ~projects/opencortex/~ directory:
-#+begin_src bash
-docker-compose up --build -d
-#+end_src
-
-** 2. Check Logs
-#+begin_src bash
-docker-compose logs -f
-#+end_src
-
-* Volume Mapping
-The ~docker-compose.yml~ file automatically mounts your host's ~memex~ directory to ~/memex~ inside the container. This allows the agent to:
-1. Read/Write to your Zettelkasten and GTD files.
-2. Maintain its local state (Memory, snapshots).
-
-* Troubleshooting
-** signal-cli Identity
-If using the Signal gateway, ensure you have registered your number via the host's ~signal-cli~ or within the container. The state is preserved in the ~signal-state~ Docker volume.
-
-** Re-loading Skills
-The container pre-caches dependencies during the build. If you modify core Lisp logic, you must rebuild the image (~--build~). If you only modify ~.org~ skills in your memex, the agent can reload them dynamically if they are part of the startup scan.

docs/quickstart.org

@@ -1,55 +0,0 @@
-#+TITLE: Quickstart Guide: The Road to Autonomousty
-#+AUTHOR: Amr
-#+DATE: [2026-04-11 Sat]
-#+FILETAGS: :quickstart:onboarding:guide:
-
-* 1. Introduction
-Welcome to ~opencortex~, the "Executive Soul" of your personal OS. This guide will help you set up and interact with your first probabilistic-deterministic agent.
-
-* 2. Prerequisites
-Before launching the harness, ensure your host environment has:
-- **Docker & Docker Compose**: The primary enclosure for the Lisp Machine.
-- **LLM API Keys**: At least one key for Gemini, Anthropic, or OpenAI.
-- **Emacs (Optional)**: For the full literate experience via ~opencortex.el~.
-
-* 3. Installation & Enclosure
-** Step 1: Clone the Autonomousty
-#+begin_src bash
-git clone https://github.com/amr/opencortex.git
-cd opencortex
-#+end_src
-
-** Step 2: Secret Configuration
-Copy the example environment file and add your keys.
-#+begin_src bash
-cp .env.example .env
-# Edit .env with your favorite editor
-#+end_src
-
-** Step 3: Launch the Image
-This will build the SBCL environment and start the Micro-Loader.
-#+begin_src bash
-docker-compose up --build -d
-#+end_src
-
-* 4. Interaction Gateways
-Once the harness is "Ready", you can interact with it via multiple sensors.
-
-** Gateway A: Emacs (communication protocol)
-If you have configured the ~opencortex~ package in Emacs:
-1. Open a chat buffer: ~M-x opencortex-chat-open~.
-2. Send: "Are you online, agent?"
-
-** Gateway B: External Sensors
-If you enabled Signal or Telegram in ~.env~, send a message directly to your bot.
-
-* 5. Verification (The Chaos Check)
-To ensure the harness is fully healthy, check the logs for the Micro-Loader summary:
-#+begin_src bash
-docker-compose logs -f opencortex
-#+end_src
-Look for: ~LOADER: Boot Complete. [Ready: 34] [Failed: 0]~
-
-* 6. Next Steps
-- **Extend the Brain**: Read the [[file:skill-creation.org][Skill Creation Guide]] to add custom Lisp skills.
-- **Deep Dive**: Explore the [[file:../literate/][literate/]] directory to understand the harness's architecture.

scripts/onboard-baremetal.sh

@@ -1,59 +0,0 @@
-#!/bin/bash
-# OpenCortex Final-Mile Installer
-RED='\033[0;31m'; GREEN='\033[0;32m'; BLUE='\033[0;34m'; YELLOW='\033[0;33m'; NC='\033[0m'
-echo -e "${BLUE}=== OpenCortex: Baremetal Power-User Setup ===${NC}"
-
-prompt_user() {
-    local prompt="$1"
-    local default="$2"
-    local var_name="$3"
-    local result=""
-    echo -n -e "${YELLOW}$prompt (default: $default): ${NC}" >&2
-    if read -t 5 result; then :; else result="$default"; echo -e "${BLUE} [Auto-Selected: $default]${NC}" >&2; fi
-    val=${result:-$default}
-    eval "$var_name=\"$val\""
-}
-
-# 1. Dependencies
-if ! command -v sbcl >/dev/null 2>&1; then
-    echo -e "${BLUE}Installing dependencies...${NC}"
-    sudo apt-get update && sudo apt-get install -y sbcl emacs git curl socat || true
-fi
-
-# 2. Quicklisp
-if [ ! -d "$HOME/quicklisp" ]; then
-    curl -O https://beta.quicklisp.org/quicklisp.lisp
-    sbcl --non-interactive --load quicklisp.lisp --eval "(quicklisp-quickstart:install)" --eval "(ql-util:without-prompting (ql:add-to-init-file))"
-    rm quicklisp.lisp
-fi
-
-# 3. Tangling
-echo -e "${BLUE}Tangling source files...${NC}"
-mkdir -p src
-for f in literate/*.org; do
-    echo "  - Tangling $f"
-    emacs --batch --eval "(require 'org)" --eval "(org-babel-tangle-file \"$f\")" >/dev/null 2>&1
-done
-
-# 4. Config
-if [ ! -f .env ]; then cp .env.example .env; fi
-prompt_user "What is your name?" "User" "USER_NAME"
-prompt_user "What shall we name your Assistant?" "OpenCortex" "AGENT_NAME"
-prompt_user "Select provider (1:Gemini, 2:OpenRouter)" "1" "LLM_CHOICE"
-
-sed -i "s/MEMEX_USER=.*/MEMEX_USER=\"$USER_NAME\"/g" .env
-sed -i "s/MEMEX_ASSISTANT=.*/MEMEX_ASSISTANT=\"$AGENT_NAME\"/g" .env
-
-# 5. Path Alignment
-INSTALL_DIR="$(cd "$(dirname "$0")/.." && pwd)"
-sed -i "s|MEMEX_DIR=.*|MEMEX_DIR=\"$(dirname "$INSTALL_DIR")\"|g" .env
-sed -i "s|SKILLS_DIR=.*|SKILLS_DIR=\"$INSTALL_DIR/skills\"|g" .env
-
-mkdir -p "$HOME/.local/bin"
-ln -sf "$INSTALL_DIR/opencortex.sh" "$HOME/.local/bin/opencortex"
-echo -e "${GREEN}✓ Installed 'opencortex' command to ~/.local/bin${NC}"
-
-echo -e "\n${GREEN}==============================================${NC}"
-echo -e "    OpenCortex Installation Complete!        "
-echo -e "==============================================${NC}"
-echo -e "To start: opencortex"

scripts/org-agent-chat.sh

@@ -1,20 +0,0 @@
-#!/bin/bash
-# opencortex-chat: The terminal mouthpiece for the Autonomous Brain.
-PORT=9105
-HOST=${1:-localhost}
-
-# Check for socat (preferred)
-if command -v socat >/dev/null 2>&1; then
-    # Use socat with READLINE for history and arrow-key support.
-    # It establishes a persistent bidirectional connection.
-    socat READLINE,history=$HOME/.org_agent_history TCP:$HOST:$PORT
-else
-    # Fallback to nc (netcat) for a single-shot connection if socat is missing.
-    # Note: This is less robust for agents with long-thinking times.
-    echo "WARNING: socat not found. Falling back to nc (no line-editing support)."
-    while true; do
-        read -p "User: " MESSAGE
-        if [ -z "$MESSAGE" ]; then continue; fi
-        echo "$MESSAGE" | nc -N $HOST $PORT
-    done
-fi

src/communication-validator.lisp

@@ -6,7 +6,7 @@
     (error "Communication Protocol Schema Error: Message must be a property list (got ~s)" (type-of msg)))
   
   (let ((type (let ((raw (proto-get msg :type))) (if (keywordp raw) (intern (string-upcase (string raw)) :keyword) raw))))
-    (unless (member type '(:REQUEST :EVENT :RESPONSE :LOG :STATUS :CHAT))
+    (unless (member type '(:REQUEST :EVENT :RESPONSE :LOG :STATUS))
       (progn (harness-log "REJECTED MSG: ~s" msg) (error "Communication Protocol Schema Error: Invalid message type '~a'" type)))
     
     (case type