diff --git a/bin/disinto b/bin/disinto
index f40d589..5487d75 100755
--- a/bin/disinto
+++ b/bin/disinto
@@ -4,12 +4,19 @@
 #
 # Commands:
 #   disinto init <repo-url> [options]   Bootstrap a new project
+#   disinto up                          Start the full stack (docker compose)
+#   disinto down                        Stop the full stack
+#   disinto logs [service]              Tail service logs
+#   disinto shell                       Shell into the agent container
 #   disinto status                      Show factory status
 #   disinto secrets <edit|show|migrate> Manage encrypted secrets
 #
 # Usage:
 #   disinto init https://github.com/user/repo
 #   disinto init user/repo --branch main --ci-id 3
+#   disinto init user/repo --bare        (bare-metal, no compose)
+#   disinto up
+#   disinto down
 #   disinto status
 # =============================================================================
 set -euo pipefail
@@ -25,6 +32,10 @@ disinto — autonomous code factory CLI
 
 Usage:
   disinto init <repo-url> [options]    Bootstrap a new project
+  disinto up                           Start the full stack (docker compose)
+  disinto down                         Stop the full stack
+  disinto logs [service]               Tail service logs
+  disinto shell                        Shell into the agent container
   disinto status                       Show factory status
   disinto secrets <edit|show|migrate>  Manage encrypted secrets (.env.enc)
 
@@ -33,6 +44,7 @@ Init options:
   --repo-root <path>   Local clone path (default: ~/name)
   --ci-id <n>          Woodpecker CI repo ID (default: 0 = no CI)
   --forge-url <url>    Forge base URL (default: http://localhost:3000)
+  --bare               Skip compose generation (bare-metal setup)
   --yes                Skip confirmation prompts
 EOF
   exit 1
@@ -136,15 +148,128 @@ write_secrets_encrypted() {
 
 FORGEJO_DATA_DIR="${HOME}/.disinto/forgejo"
 
+# Generate docker-compose.yml in the factory root.
+generate_compose() {
+  local forge_port="${1:-3000}"
+  local compose_file="${FACTORY_ROOT}/docker-compose.yml"
+
+  cat > "$compose_file" <<'COMPOSEEOF'
+# docker-compose.yml — generated by disinto init
+# Brings up Forgejo, Woodpecker, and the agent runtime.
+
+services:
+  forgejo:
+    image: forgejo/forgejo:latest
+    restart: unless-stopped
+    volumes:
+      - forgejo-data:/data
+    environment:
+      FORGEJO__database__DB_TYPE: sqlite3
+      FORGEJO__server__ROOT_URL: http://forgejo:3000/
+      FORGEJO__server__HTTP_PORT: "3000"
+      FORGEJO__service__DISABLE_REGISTRATION: "true"
+    networks:
+      - disinto-net
+
+  woodpecker:
+    image: woodpeckerci/woodpecker-server:latest
+    restart: unless-stopped
+    volumes:
+      - woodpecker-data:/var/lib/woodpecker
+    environment:
+      WOODPECKER_FORGEJO: "true"
+      WOODPECKER_FORGEJO_URL: http://forgejo:3000
+      WOODPECKER_FORGEJO_CLIENT: ${WP_FORGEJO_CLIENT:-}
+      WOODPECKER_FORGEJO_SECRET: ${WP_FORGEJO_SECRET:-}
+      WOODPECKER_HOST: http://woodpecker:8000
+      WOODPECKER_DATABASE_DRIVER: sqlite3
+      WOODPECKER_DATABASE_DATASOURCE: /var/lib/woodpecker/woodpecker.sqlite
+    depends_on:
+      - forgejo
+    networks:
+      - disinto-net
+
+  agents:
+    build: ./docker/agents
+    restart: unless-stopped
+    volumes:
+      - agent-data:/home/agent/data
+      - project-repos:/home/agent/repos
+      - ./:/home/agent/disinto:ro
+      - claude-auth:/home/agent/.claude:ro
+    environment:
+      FORGE_URL: http://forgejo:3000
+      WOODPECKER_SERVER: http://woodpecker:8000
+      DISINTO_CONTAINER: "1"
+    env_file:
+      - .env
+    depends_on:
+      - forgejo
+      - woodpecker
+    networks:
+      - disinto-net
+
+volumes:
+  forgejo-data:
+  woodpecker-data:
+  agent-data:
+  project-repos:
+  claude-auth:
+
+networks:
+  disinto-net:
+    driver: bridge
+COMPOSEEOF
+
+  # Patch the forgejo port mapping into the file if non-default
+  if [ "$forge_port" != "3000" ]; then
+    # Add port mapping to forgejo service so it's reachable from host during init
+    sed -i "/image: forgejo\/forgejo:latest/a\\    ports:\\n      - \"${forge_port}:3000\"" "$compose_file"
+  else
+    sed -i "/image: forgejo\/forgejo:latest/a\\    ports:\\n      - \"3000:3000\"" "$compose_file"
+  fi
+
+  echo "Created: ${compose_file}"
+}
+
+# Generate docker/agents/ files if they don't already exist.
+generate_agent_docker() {
+  local docker_dir="${FACTORY_ROOT}/docker/agents"
+  mkdir -p "$docker_dir"
+
+  if [ ! -f "${docker_dir}/Dockerfile" ]; then
+    echo "Warning: docker/agents/Dockerfile not found — expected in repo" >&2
+  fi
+  if [ ! -f "${docker_dir}/entrypoint.sh" ]; then
+    echo "Warning: docker/agents/entrypoint.sh not found — expected in repo" >&2
+  fi
+}
+
+# Check whether compose mode is active (docker-compose.yml exists).
+is_compose_mode() {
+  [ -f "${FACTORY_ROOT}/docker-compose.yml" ]
+}
+
 # Provision or connect to a local Forgejo instance.
 # Creates admin + bot users, generates API tokens, stores in .env.
+# When $DISINTO_BARE is set, uses standalone docker run; otherwise uses compose.
 setup_forge() {
   local forge_url="$1"
   local repo_slug="$2"
+  local use_bare="${DISINTO_BARE:-false}"
 
   echo ""
   echo "── Forge setup ────────────────────────────────────────"
 
+  # Helper: run a command inside the Forgejo container
+  _forgejo_exec() {
+    if [ "$use_bare" = true ]; then
+      docker exec disinto-forgejo "$@"
+    else
+      docker compose -f "${FACTORY_ROOT}/docker-compose.yml" exec -T forgejo "$@"
+    fi
+  }
+
   # Check if Forgejo is already running
   if curl -sf --max-time 5 "${forge_url}/api/v1/version" >/dev/null 2>&1; then
     echo "Forgejo:  ${forge_url} (already running)"
@@ -158,29 +283,33 @@ setup_forge() {
       exit 1
     fi
 
-    # Create data directory
-    mkdir -p "${FORGEJO_DATA_DIR}"
-
     # Extract port from forge_url
     local forge_port
     forge_port=$(printf '%s' "$forge_url" | sed -E 's|.*:([0-9]+)/?$|\1|')
     forge_port="${forge_port:-3000}"
 
-    # Start Forgejo container
-    if docker ps -a --format '{{.Names}}' | grep -q '^disinto-forgejo$'; then
-      docker start disinto-forgejo >/dev/null 2>&1 || true
+    if [ "$use_bare" = true ]; then
+      # Bare-metal mode: standalone docker run
+      mkdir -p "${FORGEJO_DATA_DIR}"
+
+      if docker ps -a --format '{{.Names}}' | grep -q '^disinto-forgejo$'; then
+        docker start disinto-forgejo >/dev/null 2>&1 || true
+      else
+        docker run -d \
+          --name disinto-forgejo \
+          --restart unless-stopped \
+          -p "${forge_port}:3000" \
+          -p 2222:22 \
+          -v "${FORGEJO_DATA_DIR}:/data" \
+          -e "FORGEJO__database__DB_TYPE=sqlite3" \
+          -e "FORGEJO__server__ROOT_URL=${forge_url}/" \
+          -e "FORGEJO__server__HTTP_PORT=3000" \
+          -e "FORGEJO__service__DISABLE_REGISTRATION=true" \
+          forgejo/forgejo:latest
+      fi
     else
-      docker run -d \
-        --name disinto-forgejo \
-        --restart unless-stopped \
-        -p "${forge_port}:3000" \
-        -p 2222:22 \
-        -v "${FORGEJO_DATA_DIR}:/data" \
-        -e "FORGEJO__database__DB_TYPE=sqlite3" \
-        -e "FORGEJO__server__ROOT_URL=${forge_url}/" \
-        -e "FORGEJO__server__HTTP_PORT=3000" \
-        -e "FORGEJO__service__DISABLE_REGISTRATION=true" \
-        forgejo/forgejo:latest
+      # Compose mode: start Forgejo via docker compose
+      docker compose -f "${FACTORY_ROOT}/docker-compose.yml" up -d forgejo
     fi
 
     # Wait for Forgejo to become healthy
@@ -206,7 +335,7 @@ setup_forge() {
 
   if ! curl -sf --max-time 5 "${forge_url}/api/v1/users/${admin_user}" >/dev/null 2>&1; then
     echo "Creating admin user: ${admin_user}"
-    docker exec disinto-forgejo forgejo admin user create \
+    _forgejo_exec forgejo admin user create \
       --admin \
       --username "${admin_user}" \
       --password "${admin_pass}" \
@@ -241,7 +370,7 @@ setup_forge() {
       -H "Authorization: token ${admin_token}" \
       "${forge_url}/api/v1/users/${bot_user}" >/dev/null 2>&1; then
       echo "Creating bot user: ${bot_user}"
-      docker exec disinto-forgejo forgejo admin user create \
+      _forgejo_exec forgejo admin user create \
         --username "${bot_user}" \
         --password "${bot_pass}" \
         --email "${bot_user}@disinto.local" \
@@ -748,18 +877,22 @@ disinto_init() {
   shift
 
   # Parse flags
-  local branch="" repo_root="" ci_id="0" auto_yes=false forge_url_flag=""
+  local branch="" repo_root="" ci_id="0" auto_yes=false forge_url_flag="" bare=false
   while [ $# -gt 0 ]; do
     case "$1" in
       --branch)    branch="$2"; shift 2 ;;
       --repo-root) repo_root="$2"; shift 2 ;;
       --ci-id)     ci_id="$2"; shift 2 ;;
       --forge-url) forge_url_flag="$2"; shift 2 ;;
+      --bare)      bare=true; shift ;;
       --yes)       auto_yes=true; shift ;;
       *) echo "Unknown option: $1" >&2; exit 1 ;;
     esac
   done
 
+  # Export bare-metal flag for setup_forge
+  export DISINTO_BARE="$bare"
+
   # Extract org/repo slug
   local forge_repo
   forge_repo=$(parse_repo_slug "$repo_url")
@@ -829,6 +962,15 @@ p.write_text(text)
     fi
   fi
 
+  # Generate compose files (unless --bare)
+  if [ "$bare" = false ]; then
+    local forge_port
+    forge_port=$(printf '%s' "$forge_url" | sed -E 's|.*:([0-9]+)/?$|\1|')
+    forge_port="${forge_port:-3000}"
+    generate_compose "$forge_port"
+    generate_agent_docker
+  fi
+
   # Set up local Forgejo instance (provision if needed, create users/tokens/repo)
   setup_forge "$forge_url" "$forge_repo"
 
@@ -919,11 +1061,24 @@ p.write_text(text)
   # Encrypt secrets if SOPS + age are available
   write_secrets_encrypted
 
+  # Bring up the full stack (compose mode only)
+  if [ "$bare" = false ] && [ -f "${FACTORY_ROOT}/docker-compose.yml" ]; then
+    echo ""
+    echo "── Starting full stack ────────────────────────────────"
+    docker compose -f "${FACTORY_ROOT}/docker-compose.yml" up -d
+    echo "Stack:   running (forgejo + woodpecker + agents)"
+  fi
+
   echo ""
   echo "Done. Project ${project_name} is ready."
   echo "  Config:  ${toml_path}"
   echo "  Clone:   ${repo_root}"
   echo "  Forge:   ${forge_url}/${forge_repo}"
+  if [ "$bare" = false ]; then
+    echo "  Stack:   docker compose (use 'disinto up/down/logs/shell')"
+  else
+    echo "  Mode:    bare-metal"
+  fi
   echo "  Run 'disinto status' to verify."
 }
 
@@ -1054,10 +1209,79 @@ disinto_secrets() {
   esac
 }
 
+# ── up command ────────────────────────────────────────────────────────────────
+
+disinto_up() {
+  local compose_file="${FACTORY_ROOT}/docker-compose.yml"
+  if [ ! -f "$compose_file" ]; then
+    echo "Error: docker-compose.yml not found" >&2
+    echo "  Run 'disinto init <repo-url>' first (without --bare)" >&2
+    exit 1
+  fi
+
+  # Decrypt secrets to temp .env if SOPS available and .env.enc exists
+  local tmp_env=""
+  local enc_file="${FACTORY_ROOT}/.env.enc"
+  local env_file="${FACTORY_ROOT}/.env"
+  if [ -f "$enc_file" ] && command -v sops &>/dev/null && [ ! -f "$env_file" ]; then
+    tmp_env="${env_file}"
+    sops -d --output-type dotenv "$enc_file" > "$tmp_env"
+    trap '[ -n "${tmp_env:-}" ] && rm -f "$tmp_env"' EXIT
+    echo "Decrypted secrets for compose"
+  fi
+
+  docker compose -f "$compose_file" up -d "$@"
+  echo "Stack is up"
+
+  # Clean up temp .env (also handled by EXIT trap if compose fails)
+  if [ -n "$tmp_env" ] && [ -f "$tmp_env" ]; then
+    rm -f "$tmp_env"
+    echo "Removed temporary .env"
+  fi
+}
+
+# ── down command ──────────────────────────────────────────────────────────────
+
+disinto_down() {
+  local compose_file="${FACTORY_ROOT}/docker-compose.yml"
+  if [ ! -f "$compose_file" ]; then
+    echo "Error: docker-compose.yml not found" >&2
+    exit 1
+  fi
+  docker compose -f "$compose_file" down "$@"
+  echo "Stack is down"
+}
+
+# ── logs command ──────────────────────────────────────────────────────────────
+
+disinto_logs() {
+  local compose_file="${FACTORY_ROOT}/docker-compose.yml"
+  if [ ! -f "$compose_file" ]; then
+    echo "Error: docker-compose.yml not found" >&2
+    exit 1
+  fi
+  docker compose -f "$compose_file" logs -f "$@"
+}
+
+# ── shell command ─────────────────────────────────────────────────────────────
+
+disinto_shell() {
+  local compose_file="${FACTORY_ROOT}/docker-compose.yml"
+  if [ ! -f "$compose_file" ]; then
+    echo "Error: docker-compose.yml not found" >&2
+    exit 1
+  fi
+  docker compose -f "$compose_file" exec agents bash
+}
+
 # ── Main dispatch ────────────────────────────────────────────────────────────
 
 case "${1:-}" in
   init)    shift; disinto_init "$@" ;;
+  up)      shift; disinto_up "$@" ;;
+  down)    shift; disinto_down "$@" ;;
+  logs)    shift; disinto_logs "$@" ;;
+  shell)   shift; disinto_shell ;;
   status)  shift; disinto_status "$@" ;;
   secrets) shift; disinto_secrets "$@" ;;
   -h|--help) usage ;;
diff --git a/docker/agents/Dockerfile b/docker/agents/Dockerfile
new file mode 100644
index 0000000..18cc7f2
--- /dev/null
+++ b/docker/agents/Dockerfile
@@ -0,0 +1,22 @@
+FROM debian:bookworm-slim
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    bash curl git jq tmux cron python3 openssh-client ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Claude CLI — install and verify
+RUN curl -fsSL https://cli.anthropic.com/install.sh | sh \
+    && cp "$(find /root -name claude -type f 2>/dev/null | head -1)" /usr/local/bin/claude \
+    && claude --version
+
+# Non-root user
+RUN useradd -m -u 1000 -s /bin/bash agent
+
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+
+# Entrypoint runs as root to start the cron daemon;
+# cron jobs execute as the agent user (crontab -u agent).
+WORKDIR /home/agent
+
+ENTRYPOINT ["/entrypoint.sh"]
diff --git a/docker/agents/entrypoint.sh b/docker/agents/entrypoint.sh
new file mode 100644
index 0000000..ce36e89
--- /dev/null
+++ b/docker/agents/entrypoint.sh
@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# entrypoint.sh — Start agent container with cron in foreground
+#
+# Runs as root inside the container.  Installs crontab entries for the
+# agent user from project TOMLs, then starts cron in the foreground.
+# All cron jobs execute as the agent user (UID 1000).
+
+DISINTO_DIR="/home/agent/disinto"
+LOGFILE="/home/agent/data/agent-entrypoint.log"
+mkdir -p /home/agent/data
+chown agent:agent /home/agent/data
+
+log() {
+  printf '[%s] %s\n' "$(date -u '+%Y-%m-%d %H:%M:%S UTC')" "$*" | tee -a "$LOGFILE"
+}
+
+# Build crontab from project TOMLs and install for the agent user.
+install_project_crons() {
+  local cron_lines=""
+  for toml in "${DISINTO_DIR}"/projects/*.toml; do
+    [ -f "$toml" ] || continue
+    local pname
+    pname=$(python3 -c "
+import sys, tomllib
+with open(sys.argv[1], 'rb') as f:
+    print(tomllib.load(f)['name'])
+" "$toml" 2>/dev/null) || continue
+
+    cron_lines="${cron_lines}
+# disinto: ${pname}
+2,7,12,17,22,27,32,37,42,47,52,57 * * * * ${DISINTO_DIR}/review/review-poll.sh ${toml} >/dev/null 2>&1
+4,9,14,19,24,29,34,39,44,49,54,59 * * * * ${DISINTO_DIR}/dev/dev-poll.sh ${toml} >/dev/null 2>&1
+0 0,6,12,18 * * * cd ${DISINTO_DIR} && bash gardener/gardener-run.sh ${toml} >/dev/null 2>&1"
+  done
+
+  if [ -n "$cron_lines" ]; then
+    printf '%s\n' "$cron_lines" | crontab -u agent -
+    log "Installed crontab for agent user"
+  else
+    log "No project TOMLs found — crontab empty"
+  fi
+}
+
+log "Agent container starting"
+install_project_crons
+
+# Run cron in the foreground.  Cron jobs execute as the agent user.
+log "Starting cron daemon"
+exec cron -f
diff --git a/lib/env.sh b/lib/env.sh
index f1b0bc8..72a8e0a 100755
--- a/lib/env.sh
+++ b/lib/env.sh
@@ -7,6 +7,14 @@ set -euo pipefail
 # Resolve script root (parent of lib/)
 FACTORY_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 
+# Container detection: when running inside the agent container, DISINTO_CONTAINER
+# is set by docker-compose.yml.  Adjust paths so phase files, logs, and thread
+# maps land on the persistent volume instead of /tmp (which is ephemeral).
+if [ "${DISINTO_CONTAINER:-}" = "1" ]; then
+  DISINTO_DATA_DIR="${HOME}/data"
+  mkdir -p "${DISINTO_DATA_DIR}"
+fi
+
 # Load secrets: prefer .env.enc (SOPS-encrypted), fall back to plaintext .env
 if [ -f "$FACTORY_ROOT/.env.enc" ] && command -v sops &>/dev/null; then
   set -a
@@ -123,7 +131,12 @@ wpdb() {
 # Matrix messaging helper — usage: matrix_send <prefix> <message> [thread_event_id] [context_tag]
 # Returns event_id on stdout. Registers threads for listener dispatch.
 # context_tag is stored in the thread map (e.g. issue number) for routing replies.
-MATRIX_THREAD_MAP="${MATRIX_THREAD_MAP:-/tmp/matrix-thread-map}"
+# Thread map: use persistent data dir inside container, /tmp on bare metal
+if [ "${DISINTO_CONTAINER:-}" = "1" ]; then
+  MATRIX_THREAD_MAP="${MATRIX_THREAD_MAP:-${DISINTO_DATA_DIR}/matrix-thread-map}"
+else
+  MATRIX_THREAD_MAP="${MATRIX_THREAD_MAP:-/tmp/matrix-thread-map}"
+fi
 matrix_send() {
   [ -z "${MATRIX_TOKEN:-}" ] && return 0
   local prefix="$1" msg="$2" thread_id="${3:-}" ctx_tag="${4:-}"