v0.2.1: polish, deploy, CI, and literate refactor

- Secret Exposure Gate + Privacy Filter (Bouncer)
- Shell actuator safety harness (timeout, blocked patterns)
- REPL-first enforcement (lisp validation gate, system-prompt-augment)
- Engineering Standards lifecycle (two-track Org-first + REPL-first)
- Literate Programming discipline (one function per block, reflect-back)
- AGENTS.md: thin routing layer, skills are authoritative
- SKILLS_DIR removed, ~/notes fallback eliminated
- opencortex.sh: multi-distro (Debian+Fedora), configure, install service, backup, restore, help
- infrastructure/opencortex.service (systemd user unit)
- Docker: updated to debian:trixie, fixed build context
- GitHub CI: lint + test workflows fixed, trigger on tags only
- Gitea CI: deploy workflow paths fixed
- README: one-line curl install, badges
- USER_MANUAL: Deployment section (bare metal, Docker, backup)
- .gitignore: skills/*.lisp and tests/*.lisp as generated artifacts
- Prose/block refactor across all 35 org files
- Test suite Tier 1: 43/45 pass (env-dependent failures isolated)

infrastructure/docker/Dockerfile

@@ -1,32 +1,23 @@
-FROM debian:bullseye-slim
+FROM debian:trixie-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 \
+    sbcl emacs-nox curl git socat netcat-openbsd rlwrap \
+    libssl-dev libncurses-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))" \
+    && 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
+RUN mkdir -p /root/memex && ./opencortex.sh configure --non-interactive
 
 EXPOSE 9105
 
-CMD ["./opencortex.sh", "boot"]
+CMD ["./opencortex.sh", "daemon"]

infrastructure/docker/docker-compose.yml

@@ -1,18 +1,15 @@
 services:
   opencortex:
     build:
-      context: .
-      dockerfile: Dockerfile
+      context: ../../
+      dockerfile: infrastructure/docker/Dockerfile
     container_name: opencortex
-    env_file: .env
+    env_file: ../../.env
     volumes:
-      # Mount the entire memex directory (2 levels up from projects/opencortex)
-      - ../..:/memex
-      # Ensure signal-cli state is preserved
+      - ../../../..:/memex
       - signal-state:/root/.local/share/signal-cli
     ports:
       - "${ORG_AGENT_DAEMON_PORT:-9105}:9105"
-      - "${ORG_AGENT_WEB_PORT:-8080}:8080"
     restart: unless-stopped
 
 volumes:

infrastructure/opencortex.service

@@ -0,0 +1,15 @@
+[Unit]
+Description=OpenCortex Daemon
+Documentation=https://github.com/amrgharbeia/opencortex
+After=network.target
+
+[Service]
+Type=simple
+User=%u
+ExecStart=%h/projects/opencortex/opencortex.sh daemon
+Restart=on-failure
+RestartSec=10
+WorkingDirectory=%h/projects/opencortex
+
+[Install]
+WantedBy=default.target