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/.

infrastructure_new/bare-metal/install.sh

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+#!/bin/bash
+# opencortex: Bare Metal Installation Script
+# This script sets up the opencortex daemon on a Linux host (Debian/Fedora).
+
+set -e
+
+echo "--- opencortex: Bare Metal Installation ---"
+
+# 1. Check Dependencies
+echo "[1/4] Checking dependencies..."
+for cmd in sbcl curl git ripgrep; do
+    if ! command -v $cmd &> /dev/null; then
+        echo "Error: $cmd is not installed. Please install it first."
+        exit 1
+    fi
+done
+
+# 2. Setup Quicklisp
+if [ ! -d "$HOME/quicklisp" ]; then
+    echo "[2/4] Quicklisp not found. Installing..."
+    curl -O https://beta.quicklisp.org/quicklisp.lisp
+    sbcl --non-interactive --load quicklisp.lisp --eval '(quicklisp-quickstart:install)'
+    rm quicklisp.lisp
+    echo "Quicklisp installed."
+else
+    echo "[2/4] Quicklisp already installed."
+fi
+
+# 3. Build standalone binary
+echo "[3/4] Building standalone binary..."
+PROJECT_ROOT=$(pwd)/../..
+sbcl --non-interactive \
+     --eval "(push \"$PROJECT_ROOT/\" asdf:*central-registry*)" \
+     --eval "(ql:quickload :opencortex)" \
+     --eval "(asdf:make :opencortex)"
+
+echo "Binary built: $PROJECT_ROOT/opencortex-server"
+
+# 4. Instructions for Systemd
+echo "[4/4] Installation complete."
+echo ""
+echo "To run as a systemd service:"
+echo "1. Edit opencortex.service to set correct paths."
+echo "2. sudo cp opencortex.service /etc/systemd/system/"
+echo "3. sudo systemctl daemon-reload"
+echo "4. sudo systemctl enable --now opencortex"

infrastructure_new/bare-metal/org-agent.service

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+[Unit]
+Description=opencortex: Probabilistic-Deterministic Lisp Machine Kernel
+After=network.target
+
+[Service]
+Type=simple
+# Update User and WorkingDirectory to match your local setup
+User=amr
+WorkingDirectory=/home/amr/.openclaw/workspace/memex/5_projects/opencortex
+ExecStart=/home/amr/.openclaw/workspace/memex/5_projects/opencortex/opencortex-server
+Restart=always
+RestartSec=10
+
+# Environment variables can be loaded from the .env file
+EnvironmentFile=/home/amr/.openclaw/workspace/memex/5_projects/opencortex/.env
+
+[Install]
+WantedBy=multi-user.target

infrastructure_new/docker/Dockerfile

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+FROM debian:bullseye-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y \
+    sbcl \
+    emacs-nox \
+    curl \
+    git \
+    socat \
+    netcat-openbsd \
+    libssl-dev \
+    libncurses5-dev \
+    libffi-dev \
+    zlib1g-dev \
+    libsqlite3-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Quicklisp
+RUN 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
+
+WORKDIR /app
+COPY . .
+
+# Initialize system in non-interactive mode
+RUN mkdir -p /root/memex && ./opencortex.sh setup --non-interactive
+
+EXPOSE 9105
+
+CMD ["./opencortex.sh", "boot"]

infrastructure_new/docker/docker-compose.yml

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+services:
+  opencortex:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    container_name: opencortex
+    env_file: .env
+    volumes:
+      # Mount the entire memex directory (2 levels up from projects/opencortex)
+      - ../..:/memex
+      # Ensure signal-cli state is preserved
+      - signal-state:/root/.local/share/signal-cli
+    ports:
+      - "${ORG_AGENT_DAEMON_PORT:-9105}:9105"
+      - "${ORG_AGENT_WEB_PORT:-8080}:8080"
+    restart: unless-stopped
+
+volumes:
+  signal-state:

infrastructure_new/guix/manifest.scm

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+;; opencortex: Guix Environment Manifest
+;; Usage: guix shell -m manifest.scm -- sbcl --eval ...
+
+(specifications->manifest
+ '("sbcl"
+   "sbcl-cl-json"
+   "sbcl-bordeaux-threads"
+   "sbcl-usocket"
+   "sbcl-dexador"
+   "sbcl-cl-ppcre"
+   "ripgrep"
+   "git"
+   "curl"
+   "sqlite"))

infrastructure_new/lxc/setup.org

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+#+TITLE: LXC / Systemd-nspawn Deployment Guide
+#+AUTHOR: opencortex
+
+* Overview
+For users who prefer containerization without the overhead or dependency on the Docker daemon, `opencortex` can be run within a standard Linux Container (LXC) or a systemd-nspawn container.
+
+* Systemd-nspawn Setup (Fastest for Linux users)
+
+1. **Create the container root:**
+   #+begin_src bash
+   sudo debootstrap --arch=amd64 bookworm /var/lib/machines/opencortex
+   #+end_src
+
+2. **Start and enter the container:**
+   #+begin_src bash
+   sudo systemd-nspawn -D /var/lib/machines/opencortex
+   #+end_src
+
+3. **Install dependencies (inside container):**
+   #+begin_src bash
+   apt-get update && apt-get install -y sbcl curl git ripgrep libsqlite3-dev build-essential
+   #+end_src
+
+4. **Bind mount the Memex directory:**
+   Add this to your container startup or use the `--bind` flag:
+   #+begin_src bash
+   sudo systemd-nspawn -D /var/lib/machines/opencortex --bind /home/amr/.openclaw/workspace/memex
+   #+end_src
+
+* Proxmox LXC Setup
+1. Create a new LXC container using the Debian 12 template.
+2. Ensure the network is bridged so Emacs can reach it.
+3. Run the `deploy/bare-metal/install.sh` script inside the container.

infrastructure_new/vms/debian/Vagrantfile

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+Vagrant.configure("2") do |config|
+  config.vm.box = "debian/bookworm64"
+  config.vm.network "forwarded_port", guest: 9105, host: 9105
+
+  config.vm.provider "virtualbox" do |vb|
+    vb.memory = "1024"
+    vb.cpus = 2
+  end
+
+  config.vm.provision "shell", inline: <<-SHELL
+    apt-get update
+    apt-get install -y sbcl curl git ripgrep libsqlite3-dev build-essential
+    
+    # Setup for opencortex
+    mkdir -p /home/vagrant/opencortex
+    cp -r /vagrant/* /home/vagrant/opencortex/
+    chown -R vagrant:vagrant /home/vagrant/opencortex
+    
+    # Build binary natively
+    sudo -u vagrant bash -c "cd /home/vagrant/opencortex && ./deploy/bare-metal/install.sh"
+  SHELL
+end

infrastructure_new/vms/fedora/Vagrantfile

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+Vagrant.configure("2") do |config|
+  config.vm.box = "fedora/39-cloud-base"
+  config.vm.network "forwarded_port", guest: 9105, host: 9105
+
+  config.vm.provider "virtualbox" do |vb|
+    vb.memory = "1024"
+    vb.cpus = 2
+  end
+
+  config.vm.provision "shell", inline: <<-SHELL
+    dnf install -y sbcl curl git ripgrep sqlite-devel make gcc
+    
+    # Setup for opencortex
+    mkdir -p /home/vagrant/opencortex
+    cp -r /vagrant/* /home/vagrant/opencortex/
+    chown -R vagrant:vagrant /home/vagrant/opencortex
+    
+    # Build binary natively
+    sudo -u vagrant bash -c "cd /home/vagrant/opencortex && ./deploy/bare-metal/install.sh"
+  SHELL
+end