#+TITLE: Zero-to-One Setup (setup.org)
#+AUTHOR: Amr
#+FILETAGS: :harness:setup:
#+STARTUP: content

* Zero-to-One Setup (setup.org)
The ~setup.org~ file defines the automated installation and initialization sequence for the OpenCortex.

** The Installer Script (opencortex.sh)
#+begin_src bash :tangle ../opencortex.sh
#!/bin/bash
set -e

PORT=9105
HOST="localhost"
RED='\033[0;31m'; GREEN='\033[0;32m'; BLUE='\033[0;34m'; YELLOW='\033[0;33m'; NC='\033[0m'

command_exists() { command -v "$1" >/dev/null 2>&1; }

# Resolve symlinks to find the actual repository location
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do
    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
    SOURCE="$(readlink "$SOURCE")"
    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
done
export SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

# Load environment variables if they exist
if [ -f "$SCRIPT_DIR/.env" ]; then
    while IFS="=" read -r key value || [ -n "$key" ]; do
        if [[ $key =~ ^[a-zA-Z_][a-zA-Z0-9_]*$ ]]; then
            val=$(echo "$value" | sed "s/^\"//;s/\"$//")
            export "$key=$val"
        fi
    done < "$SCRIPT_DIR/.env"
    [ -n "$ORG_AGENT_DAEMON_PORT" ] && PORT=$ORG_AGENT_DAEMON_PORT
    [ -n "$DAEMON_HOST" ] && HOST=$DAEMON_HOST
fi

# --- 1. BOOTSTRAP ---
# If the script is run standalone, it clones the full repo and restarts itself.
if [ ! -d "$SCRIPT_DIR/.git" ] && [ ! -d "$HOME/.opencortex" ] && [[ ! "$(pwd)" =~ "opencortex" ]]; then
    echo -e "${BLUE}=== OpenCortex: Zero-to-One Bootstrapper ===${NC}"
    git clone ssh://git@10.10.10.201:2222/amr/opencortex.git ~/.opencortex
    cd ~/.opencortex && git submodule update --init --recursive
    exec ./opencortex.sh "$@"
fi

# --- 2. SETUP ---
setup_system() {
    NON_INTERACTIVE=false
    for arg in "$@"; do
        if [ "$arg" == "--non-interactive" ]; then NON_INTERACTIVE=true; fi
    done

    echo -e "${BLUE}=== OpenCortex: Initializing System ===${NC}"
    echo -e "${YELLOW}--- Installing System Dependencies ---${NC}"
    if command_exists apt-get; then
        sudo apt-get update && sudo apt-get install -y sbcl emacs-nox rlwrap netcat-openbsd curl git socat libssl-dev libncurses5-dev libffi-dev zlib1g-dev libsqlite3-dev
    fi
    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

    cd "$SCRIPT_DIR"
    if [ ! -f .env ]; then
        if [ "$NON_INTERACTIVE" = true ]; then
            echo "Non-interactive mode: Using environment variables for .env creation."
            cp .env.example .env
            [ -n "$MEMEX_USER" ] && sed -i "s|MEMEX_USER=.*|MEMEX_USER=\"$MEMEX_USER\"|" .env
            [ -n "$MEMEX_ASSISTANT" ] && sed -i "s|MEMEX_ASSISTANT=.*|MEMEX_ASSISTANT=\"$MEMEX_ASSISTANT\"|" .env
            [ -n "$OPENROUTER_API_KEY" ] && sed -i "s|OPENROUTER_API_KEY=.*|OPENROUTER_API_KEY=\"$OPENROUTER_API_KEY\"|" .env
            [ -n "$MEMEX_DIR" ] && sed -i "s|MEMEX_DIR=.*|MEMEX_DIR=\"$MEMEX_DIR\"|" .env
        else
            cp .env.example .env
            echo -e "\n${YELLOW}--- Identity Configuration ---${NC}"
            read -p "Your Name [User]: " user_name < /dev/tty
            user_name=${user_name:-User}
            sed -i "s|MEMEX_USER=.*|MEMEX_USER=\"$user_name\"|" .env

            read -p "Agent Name [OpenCortex]: " agent_name < /dev/tty
            agent_name=${agent_name:-OpenCortex}
            sed -i "s|MEMEX_ASSISTANT=.*|MEMEX_ASSISTANT=\"$agent_name\"|" .env

            echo -e "\n${YELLOW}--- LLM Configuration ---${NC}"
            read -p "OpenRouter API Key: " openrouter_key < /dev/tty
            [ -n "$openrouter_key" ] && sed -i "s|OPENROUTER_API_KEY=.*|OPENROUTER_API_KEY=\"$openrouter_key\"|" .env

            echo -e "\n${YELLOW}--- Memex Folder Structure ---${NC}"
            read -p "Memex Root [\$HOME/memex]: " memex_dir < /dev/tty
            memex_dir=${memex_dir:-\$HOME/memex}
            sed -i "s|MEMEX_DIR=.*|MEMEX_DIR=\"$memex_dir\"|" .env
        fi

        # Hydrate default paths
        M_DIR=$(grep MEMEX_DIR .env | cut -d'"' -f2 | sed "s|\$HOME|$HOME|")
        sed -i "s|SKILLS_DIR=.*|SKILLS_DIR=\"$SCRIPT_DIR/skills\"|" .env
        sed -i "s|ZETTELKASTEN_DIR=.*|ZETTELKASTEN_DIR=\"$M_DIR/notes\"|" .env
        mkdir -p "$M_DIR" "$M_DIR/notes" "$M_DIR/areas" "$M_DIR/resources" "$M_DIR/archives" "$M_DIR/system" "$M_DIR/inbox" "$M_DIR/daily" "$M_DIR/projects"
    fi

    mkdir -p src
    for f in literate/*.org; do
        emacs --batch --eval "(require 'org)" --eval "(org-babel-tangle-file \"$f\")" >/dev/null 2>&1 || true
    done

    mkdir -p "$HOME/.local/bin"
    ln -sf "$SCRIPT_DIR/opencortex.sh" "$HOME/.local/bin/opencortex"

    for shell_config in "$HOME/.bashrc" "$HOME/.profile"; do
        if [ -f "$shell_config" ]; then
            if ! grep -q ".local/bin" "$shell_config"; then
                echo 'export PATH="$HOME/.local/bin:$PATH"' >> "$shell_config"
            fi
        fi
    done
    export PATH="$HOME/.local/bin:$PATH"

    echo -e "${YELLOW}--- Compiling and Loading OpenCortex ---${NC}"
    sbcl --non-interactive --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' --eval '(push (truename (uiop:getenv "SCRIPT_DIR")) asdf:*central-registry*)' --eval "(ql:quickload '(:opencortex :croatoan))"

    if [ $? -ne 0 ]; then
        echo -e "${RED}✗ Compilation failed.${NC}"
        exit 1
    fi

    if [ "$NON_INTERACTIVE" = true ]; then
        echo "Setup complete (Non-interactive)."
        exit 0
    fi

    echo -e "${YELLOW}--- Finalizing: Awakening the Brain ---${NC}"
    "$SCRIPT_DIR/opencortex.sh" --boot > "$SCRIPT_DIR/brain.log" 2>&1 &

    success=false
    for i in {1..30}; do
        if nc -z localhost $PORT 2>/dev/null; then success=true; break; fi
        sleep 2
        echo -n "."
    done

    if [ "$success" = true ]; then
        echo -e "\n${GREEN}✓ Brain is alive on port $PORT.${NC}"
        exit 0
    else
        echo -e "\n${RED}✗ Brain failed to wake up.${NC}"
        exit 1
    fi
}

# --- 3. COMMAND ROUTER ---
COMMAND=$1
[ -z "$COMMAND" ] && COMMAND="cli"
shift || true

DEFAULT_PORT=9105
DEFAULT_HOST="localhost"
TARGET_PORT=${PORT:-$DEFAULT_PORT}
TARGET_HOST=${HOST:-$DEFAULT_HOST}

# If uninitialized, force setup.
if [ ! -f "$SCRIPT_DIR/src/package.lisp" ] || [ ! -f "$SCRIPT_DIR/.env" ]; then
    COMMAND="setup"
fi

case "$COMMAND" in
    setup)
        setup_system "$@"
        ;;

    --boot|boot)
        export SKILLS_DIR="${SCRIPT_DIR}/skills"
        [ -z "$MEMEX_DIR" ] && export MEMEX_DIR="$HOME/memex"
        if [ -f "$SCRIPT_DIR/.env" ]; then
           export OPENROUTER_API_KEY=$(grep OPENROUTER_API_KEY "$SCRIPT_DIR/.env" | cut -d'"' -f2)
        fi
        exec sbcl --non-interactive --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' --eval '(setf *debugger-hook* (lambda (c h) (declare (ignore h)) (format *error-output* "FATAL LISP ERROR: ~a~%" c) (uiop:print-backtrace :stream *error-output*) (uiop:quit 1)))' --eval '(push (truename (uiop:getenv "SCRIPT_DIR")) asdf:*central-registry*)' --eval '(format t "--- Quickloading OpenCortex ---~%")' --eval "(ql:quickload '(:opencortex :croatoan))" --eval '(opencortex:main)'
        ;;

    tui)
        if ! nc -z $TARGET_HOST $TARGET_PORT 2>/dev/null; then
            echo -e "Brain is offline. Awakening..."
            "$SCRIPT_DIR/opencortex.sh" --boot > "$SCRIPT_DIR/brain.log" 2>&1 &
            for i in {1..15}; do
                sleep 2
                if nc -z $TARGET_HOST $TARGET_PORT 2>/dev/null; then break; fi
                echo -n "."
            done
            echo ""
        fi
        echo -e "Launching Croatoan TUI..."
        export SKILLS_DIR="${SCRIPT_DIR}/skills"
        [ -z "$MEMEX_DIR" ] && export MEMEX_DIR="$HOME/memex"
        exec sbcl --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' --eval '(push (truename (uiop:getenv "SCRIPT_DIR")) asdf:*central-registry*)' --eval '(ql:quickload :opencortex/tui)' --eval '(opencortex.tui:main)'
        ;;

    cli)
        if ! nc -z $TARGET_HOST $TARGET_PORT 2>/dev/null; then
            echo -e "Brain is offline. Awakening..."
            "$SCRIPT_DIR/opencortex.sh" --boot > "$SCRIPT_DIR/brain.log" 2>&1 &
            for i in {1..15}; do
                sleep 2
                if nc -z $TARGET_HOST $TARGET_PORT 2>/dev/null; then break; fi
                echo -n "."
            done
            echo ""
        fi
        if command_exists socat; then
            exec socat - TCP:$TARGET_HOST:$TARGET_PORT
        else
            exec nc $TARGET_HOST $TARGET_PORT
        fi
        ;;

    *)
        echo -e "Unknown command: $COMMAND"
        echo "Available commands: setup, boot, tui, cli"
        exit 1
        ;;
esac
#+end_src

** Metabolic Docker Infrastructure (Dockerfile)
#+begin_src dockerfile :tangle ../Dockerfile
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"]
#+end_src