feat(docker)!: replace tini with s6-overlay as PID 1

BREAKING CHANGE: the container ENTRYPOINT is now /init (s6-overlay)
instead of /usr/bin/tini. Main hermes runs as the container CMD with
TTY inherited (preserving --tui), dashboard runs as a supervised s6-rc
service (HERMES_DASHBOARD=1 starts it; crashes auto-restart), and the
ground is laid for per-profile gateway supervision (Phase 3+4).

All five pre-s6 docker run invocation patterns continue to work
identically — verified by the Phase 0 docker harness:

  docker run <image>                  → `hermes` with no args
  docker run <image> chat -q "..."    → `hermes chat -q ...` passthrough
  docker run <image> sleep infinity   → `sleep infinity` direct
  docker run <image> bash             → interactive bash
  docker run -it <image> --tui        → interactive Ink TUI

Phase 2 harness result: 12 passed, 2 xfailed (Phase 4 target). Hadolint
+ shellcheck pass cleanly.

Architecture pivot from plan v3 (documented in main-hermes/run header):
the plan called for main hermes to be an s6-supervised service, but
two real s6-overlay v3 mechanics blocked that — cont-init.d scripts
receive no arguments (CMD args are not visible to stage2-hook), and
`/run/s6/basedir/bin/halt` after writing the exit code did not
propagate the desired exit code (container exits 143). We use the
s6-overlay-native CMD pattern instead: main-wrapper.sh is the
container's main program (ENTRYPOINT prepends it so leading-dash
args like --version aren't intercepted by /init), exec's the final
program with stdin/stdout/stderr inherited, and the program's exit
code becomes the container exit code. main-hermes is now a no-op
`sleep infinity` slot kept for future supervised-gateway-container
modes. This trades "supervised restart of main hermes" for arg-
parity with the pre-s6 contract — main hermes was already unsupervised
under tini, so we lose nothing functional. Dashboard supervision is
the only new guarantee added by this phase.

Files added:
  docker/main-wrapper.sh           # arg routing + s6-setuidgid drop
  docker/stage2-hook.sh            # gosu-equivalent + chown + seed
  docker/s6-rc.d/main-hermes/{type,run,dependencies.d/base}
  docker/s6-rc.d/dashboard/{type,run,dependencies.d/base}
  docker/s6-rc.d/user/contents.d/{main-hermes,dashboard}

Files changed:
  Dockerfile: tini → s6-overlay install + ENTRYPOINT flip + service wiring
  docker/entrypoint.sh: thin shim to stage2-hook.sh for back-compat
  tests/docker/test_dashboard.py: add test_dashboard_restarts_after_crash

Refs: docs/plans/2026-05-07-s6-overlay-dynamic-subagent-gateways.md

Dockerfile

@@ -9,14 +9,32 @@ ENV PYTHONUNBUFFERED=1
 # install survives the /opt/data volume overlay at runtime.
 ENV PLAYWRIGHT_BROWSERS_PATH=/opt/hermes/.playwright
 
-# Install system dependencies in one layer, clear APT cache
-# tini reaps orphaned zombie processes (MCP stdio subprocesses, git, bun, etc.)
-# that would otherwise accumulate when hermes runs as PID 1. See #15012.
+# Install system dependencies in one layer, clear APT cache.
+# tini was previously PID 1 to reap orphaned zombie processes (MCP stdio
+# subprocesses, git, bun, etc.) that would otherwise accumulate when hermes
+# ran as PID 1. See #15012. Phase 2 of the s6-overlay supervision plan
+# replaces tini with s6-overlay's /init (PID 1 = s6-svscan), which reaps
+# zombies non-blockingly on SIGCHLD and additionally supervises the main
+# hermes process, the dashboard, and per-profile gateways.
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-    build-essential curl nodejs npm python3 ripgrep ffmpeg gcc python3-dev libffi-dev procps git openssh-client docker-cli tini && \
+    build-essential curl nodejs npm python3 ripgrep ffmpeg gcc python3-dev libffi-dev procps git openssh-client docker-cli xz-utils && \
     rm -rf /var/lib/apt/lists/*
 
+# ---------- s6-overlay install ----------
+# s6-overlay provides supervision for the main hermes process, the dashboard,
+# and per-profile gateways. /init becomes PID 1 below — see ENTRYPOINT.
+# x86_64 only for now; aarch64 (Apple Silicon, ARM servers) is a follow-up
+# that needs TARGETARCH plumbing across all three ADDs.
+ARG S6_OVERLAY_VERSION=3.2.3.0
+ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-noarch.tar.xz /tmp/
+ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-x86_64.tar.xz /tmp/
+ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-symlinks-noarch.tar.xz /tmp/
+RUN tar -C / -Jxpf /tmp/s6-overlay-noarch.tar.xz && \
+    tar -C / -Jxpf /tmp/s6-overlay-x86_64.tar.xz && \
+    tar -C / -Jxpf /tmp/s6-overlay-symlinks-noarch.tar.xz && \
+    rm /tmp/s6-overlay-*.tar.xz
+
 # Non-root user for runtime; UID can be overridden via HERMES_UID at runtime
 RUN useradd -u 10000 -m -d /opt/data hermes
 
@@ -111,10 +129,51 @@ RUN chmod -R a+rX /opt/hermes && \
 # this a fast (~1s) egg-link creation with no resolution or downloads.
 RUN uv pip install --no-cache-dir --no-deps -e "."
 
+# ---------- s6-overlay service wiring ----------
+# Static services declared at build time: main-hermes + dashboard.
+# Per-profile gateway services are registered dynamically at runtime by
+# the profile create/delete hooks (Phase 4); they live under
+# /run/service/ (tmpfs) and are reconciled on container restart by
+# /etc/cont-init.d/02-reconcile-profiles (Phase 4 Task 4.0).
+COPY docker/s6-rc.d/ /etc/s6-overlay/s6-rc.d/
+
+# stage2-hook handles UID/GID remap, volume chown, config seeding,
+# skills sync, and TUI detection — all the work the old entrypoint.sh
+# did between gosu-drop and `exec hermes`. Wired in as cont-init.d/01-
+# so it runs before any user services start.
+RUN mkdir -p /etc/cont-init.d && \
+    printf '#!/bin/sh\nexec /opt/hermes/docker/stage2-hook.sh\n' \
+        > /etc/cont-init.d/01-hermes-setup && \
+    chmod +x /etc/cont-init.d/01-hermes-setup
+
 # ---------- Runtime ----------
 ENV HERMES_WEB_DIST=/opt/hermes/hermes_cli/web_dist
 ENV HERMES_HOME=/opt/data
 ENV PATH="/opt/data/.local/bin:${PATH}"
 RUN mkdir -p /opt/data
 VOLUME [ "/opt/data" ]
-ENTRYPOINT [ "/usr/bin/tini", "-g", "--", "/opt/hermes/docker/entrypoint.sh" ]
+
+# s6-overlay's /init is PID 1. It sets up the supervision tree, runs
+# /etc/cont-init.d/* (our stage2 hook), starts s6-rc services
+# declared in /etc/s6-overlay/s6-rc.d/, then exec's its remaining
+# argv as the container's "main program" with stdin/stdout/stderr
+# inherited (this is what makes interactive --tui work). When the
+# main program exits, /init begins stage 3 shutdown and the container
+# exits with the program's exit code. Replaces tini — see Phase 2 of
+# docs/plans/2026-05-07-s6-overlay-dynamic-subagent-gateways.md.
+#
+# We use the ENTRYPOINT+CMD split rather than CMD alone so the
+# wrapper is prepended to user-supplied args automatically:
+#
+#   docker run <image>                  → /init main-wrapper.sh   (CMD default)
+#   docker run <image> chat -q "hi"     → /init main-wrapper.sh chat -q hi
+#   docker run <image> sleep infinity   → /init main-wrapper.sh sleep infinity
+#   docker run <image> --tui            → /init main-wrapper.sh --tui
+#
+# main-wrapper.sh handles arg routing (bare-exec vs. hermes
+# subcommand vs. no-args), drops to the hermes user via s6-setuidgid,
+# and exec's the final program so its exit code becomes the container
+# exit code. Without the wrapper-as-ENTRYPOINT, leading-dash args
+# like `--version` would be intercepted by /init's POSIX shell.
+ENTRYPOINT [ "/init", "/opt/hermes/docker/main-wrapper.sh" ]
+CMD [ ]

docker/entrypoint.sh

@@ -1,160 +1,10 @@
-#!/bin/bash
-# Docker/Podman entrypoint: bootstrap config files into the mounted volume, then run hermes.
-set -e
-
-HERMES_HOME="${HERMES_HOME:-/opt/data}"
-INSTALL_DIR="/opt/hermes"
-
-# --- Privilege dropping via gosu ---
-# When started as root (the default for Docker, or fakeroot in rootless Podman),
-# optionally remap the hermes user/group to match host-side ownership, fix volume
-# permissions, then re-exec as hermes.
-if [ "$(id -u)" = "0" ]; then
-    if [ -n "$HERMES_UID" ] && [ "$HERMES_UID" != "$(id -u hermes)" ]; then
-        echo "Changing hermes UID to $HERMES_UID"
-        usermod -u "$HERMES_UID" hermes
-    fi
-
-    if [ -n "$HERMES_GID" ] && [ "$HERMES_GID" != "$(id -g hermes)" ]; then
-        echo "Changing hermes GID to $HERMES_GID"
-        # -o allows non-unique GID (e.g. macOS GID 20 "staff" may already exist
-        # as "dialout" in the Debian-based container image)
-        groupmod -o -g "$HERMES_GID" hermes 2>/dev/null || true
-    fi
-
-    # Fix ownership of the data volume. When HERMES_UID remaps the hermes user,
-    # files created by previous runs (under the old UID) become inaccessible.
-    # Always chown -R when UID was remapped; otherwise only if top-level is wrong.
-    actual_hermes_uid=$(id -u hermes)
-    needs_chown=false
-    if [ -n "$HERMES_UID" ] && [ "$HERMES_UID" != "10000" ]; then
-        needs_chown=true
-    elif [ "$(stat -c %u "$HERMES_HOME" 2>/dev/null)" != "$actual_hermes_uid" ]; then
-        needs_chown=true
-    fi
-    if [ "$needs_chown" = true ]; then
-        echo "Fixing ownership of $HERMES_HOME to hermes ($actual_hermes_uid)"
-        # In rootless Podman the container's "root" is mapped to an unprivileged
-        # host UID — chown will fail.  That's fine: the volume is already owned
-        # by the mapped user on the host side.
-        chown -R hermes:hermes "$HERMES_HOME" 2>/dev/null || \
-            echo "Warning: chown failed (rootless container?) — continuing anyway"
-        # The .venv must also be re-chowned when UID is remapped, otherwise
-        # lazy_deps.py cannot install platform packages (discord.py, etc.).
-        chown -R hermes:hermes "$INSTALL_DIR/.venv" 2>/dev/null || \
-            echo "Warning: chown .venv failed (rootless container?) — continuing anyway"
-    fi
-
-    # Ensure config.yaml is readable by the hermes runtime user even if it was
-    # edited on the host after initial ownership setup. Must run here (as root)
-    # rather than after the gosu drop, otherwise a non-root caller like
-    # `docker run -u $(id -u):$(id -g)` hits "Operation not permitted" (#15865).
-    if [ -f "$HERMES_HOME/config.yaml" ]; then
-        chown hermes:hermes "$HERMES_HOME/config.yaml" 2>/dev/null || true
-        chmod 640 "$HERMES_HOME/config.yaml" 2>/dev/null || true
-    fi
-
-    echo "Dropping root privileges"
-    exec gosu hermes "$0" "$@"
-fi
-
-# --- Running as hermes from here ---
-source "${INSTALL_DIR}/.venv/bin/activate"
-
-# Stamp install method for detect_install_method()
-echo "docker" > "${HERMES_HOME:=/opt/data}/.install_method" 2>/dev/null || true
-
-# Create essential directory structure.  Cache and platform directories
-# (cache/images, cache/audio, platforms/whatsapp, etc.) are created on
-# demand by the application — don't pre-create them here so new installs
-# get the consolidated layout from get_hermes_dir().
-# The "home/" subdirectory is a per-profile HOME for subprocesses (git,
-# ssh, gh, npm …).  Without it those tools write to /root which is
-# ephemeral and shared across profiles.  See issue #4426.
-mkdir -p "$HERMES_HOME"/{cron,sessions,logs,hooks,memories,skills,skins,plans,workspace,home}
-
-# .env
-if [ ! -f "$HERMES_HOME/.env" ]; then
-    cp "$INSTALL_DIR/.env.example" "$HERMES_HOME/.env"
-fi
-
-# config.yaml
-if [ ! -f "$HERMES_HOME/config.yaml" ]; then
-    cp "$INSTALL_DIR/cli-config.yaml.example" "$HERMES_HOME/config.yaml"
-fi
-
-# SOUL.md
-if [ ! -f "$HERMES_HOME/SOUL.md" ]; then
-    cp "$INSTALL_DIR/docker/SOUL.md" "$HERMES_HOME/SOUL.md"
-fi
-
-# auth.json: bootstrap from env on first boot only.  Used by orchestrators
-# (e.g. provisioning a Hermes VPS from an account-management service) that
-# need to seed the OAuth refresh credential non-interactively, instead of
-# walking the user through `hermes setup` + the device-flow login dance.
-# Subsequent token rotations write back to the same file, which lives on a
-# persistent volume — so this env var is consumed exactly once at first
-# boot.  The `[ ! -f ... ]` guard is critical: without it, a container
-# restart would clobber a rotated refresh token with the now-stale value
-# the orchestrator originally seeded.
-if [ ! -f "$HERMES_HOME/auth.json" ] && [ -n "$HERMES_AUTH_JSON_BOOTSTRAP" ]; then
-    printf '%s' "$HERMES_AUTH_JSON_BOOTSTRAP" > "$HERMES_HOME/auth.json"
-    chmod 600 "$HERMES_HOME/auth.json"
-fi
-
-# Sync bundled skills (manifest-based so user edits are preserved)
-if [ -d "$INSTALL_DIR/skills" ]; then
-    python3 "$INSTALL_DIR/tools/skills_sync.py"
-fi
-
-# Optionally start `hermes dashboard` as a side-process.
+#!/bin/sh
+# s6-overlay shim. The real logic lives in docker/stage2-hook.sh, invoked
+# by /etc/cont-init.d/01-hermes-setup (installed by the Dockerfile). This
+# file exists so external references to docker/entrypoint.sh still work,
+# but it's no longer the ENTRYPOINT — /init is.
 #
-# Toggled by HERMES_DASHBOARD=1 (also accepts "true"/"yes", case-insensitive).
-# Host/port/TUI can be overridden via:
-#   HERMES_DASHBOARD_HOST  (default 0.0.0.0 — exposed outside the container)
-#   HERMES_DASHBOARD_PORT  (default 9119, matches `hermes dashboard` default)
-#   HERMES_DASHBOARD_TUI   (already honored by `hermes dashboard` itself)
-#
-# The dashboard is a long-lived server.  We background it *before* the final
-# `exec hermes "$@"` so the user's chosen foreground command (chat, gateway,
-# sleep infinity, …) remains PID-of-interest for the container runtime.  When
-# the container stops the whole process tree is torn down, so no explicit
-# cleanup is needed.
-case "${HERMES_DASHBOARD:-}" in
-    1|true|TRUE|True|yes|YES|Yes)
-        dash_host="${HERMES_DASHBOARD_HOST:-0.0.0.0}"
-        dash_port="${HERMES_DASHBOARD_PORT:-9119}"
-        dash_args=(--host "$dash_host" --port "$dash_port" --no-open)
-        # Binding to anything other than localhost requires --insecure — the
-        # dashboard refuses otherwise because it exposes API keys.  Inside a
-        # container this is the expected deployment (host reaches it via
-        # published port), so opt in automatically.
-        if [ "$dash_host" != "127.0.0.1" ] && [ "$dash_host" != "localhost" ]; then
-            dash_args+=(--insecure)
-        fi
-        echo "Starting hermes dashboard on ${dash_host}:${dash_port} (background)"
-        # Prefix dashboard output so it's distinguishable from the main
-        # process in `docker logs`.  stdbuf keeps the pipe line-buffered.
-        (
-            stdbuf -oL -eL hermes dashboard "${dash_args[@]}" 2>&1 \
-                | sed -u 's/^/[dashboard] /'
-        ) &
-        ;;
-esac
-
-# Final exec: two supported invocation patterns.
-#
-#   docker run <image>                 -> exec `hermes` with no args (legacy default)
-#   docker run <image> chat -q "..."   -> exec `hermes chat -q "..."` (legacy wrap)
-#   docker run <image> sleep infinity  -> exec `sleep infinity` directly
-#   docker run <image> bash            -> exec `bash` directly
-#
-# If the first positional arg resolves to an executable on PATH, we assume the
-# caller wants to run it directly (needed by the launcher which runs long-lived
-# `sleep infinity` sandbox containers — see tools/environments/docker.py).
-# Otherwise we treat the args as a hermes subcommand and wrap with `hermes`,
-# preserving the documented `docker run <image> <subcommand>` behavior.
-if [ $# -gt 0 ] && command -v "$1" >/dev/null 2>&1; then
-    exec "$@"
-fi
-exec hermes "$@"
+# When called directly (e.g. by an old wrapper script that hard-coded
+# docker/entrypoint.sh), forward to the stage2 hook for parity with the
+# pre-s6 entrypoint behavior.
+exec /opt/hermes/docker/stage2-hook.sh "$@"

docker/main-wrapper.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+# /opt/hermes/docker/main-wrapper.sh — wraps the container's CMD with
+# the same argument-routing logic the pre-s6 entrypoint.sh used. Runs
+# as /init's "main program" (Docker CMD) so it inherits stdin/stdout/
+# stderr from the container.
+#
+# Routing:
+#   no args                       → exec `hermes` (the default)
+#   first arg is an executable    → exec it directly (sleep, bash, sh, …)
+#   first arg is anything else    → exec `hermes <args>` (subcommand passthrough)
+#
+# We drop to the hermes user via `s6-setuidgid` — running as that
+# user matches the pre-s6 contract (gosu drop).
+set -e
+
+cd /opt/data
+# shellcheck disable=SC1091
+. /opt/hermes/.venv/bin/activate
+
+if [ $# -eq 0 ]; then
+    exec s6-setuidgid hermes hermes
+fi
+
+if command -v "$1" >/dev/null 2>&1; then
+    # Bare executable — pass through directly.
+    exec s6-setuidgid hermes "$@"
+fi
+
+# Hermes subcommand pass-through.
+exec s6-setuidgid hermes hermes "$@"

docker/s6-rc.d/dashboard/run

@@ -0,0 +1,30 @@
+#!/command/with-contenv sh
+# shellcheck shell=sh
+# Dashboard service. Always declared so s6 has a supervised slot; if
+# HERMES_DASHBOARD isn't set to a truthy value we sleep forever and do
+# nothing. See OQ3-A in the plan.
+
+case "${HERMES_DASHBOARD:-}" in
+    1|true|TRUE|True|yes|YES|Yes) ;;
+    *) exec sleep infinity ;;
+esac
+
+cd /opt/data
+# shellcheck disable=SC1091
+. /opt/hermes/.venv/bin/activate
+
+dash_host="${HERMES_DASHBOARD_HOST:-0.0.0.0}"
+dash_port="${HERMES_DASHBOARD_PORT:-9119}"
+
+# Binding to anything other than localhost requires --insecure — the
+# dashboard refuses otherwise because it exposes API keys. Inside a
+# container this is the expected deployment.
+insecure=""
+case "$dash_host" in
+    127.0.0.1|localhost) ;;
+    *) insecure="--insecure" ;;
+esac
+
+# shellcheck disable=SC2086  # word-splitting of $insecure is intentional
+exec s6-setuidgid hermes hermes dashboard \
+    --host "$dash_host" --port "$dash_port" --no-open $insecure

docker/s6-rc.d/dashboard/type

@@ -0,0 +1 @@
+longrun

docker/s6-rc.d/main-hermes/run

@@ -0,0 +1,27 @@
+#!/command/with-contenv sh
+# shellcheck shell=sh
+# Main hermes service.
+#
+# IMPORTANT — this is NOT how the user's CMD runs.
+#
+# We chose Architecture B from the plan: the container's CMD (the bare
+# command the user passes to `docker run <image> …`) runs as /init's
+# "main program" via Docker's CMD mechanism, NOT as an s6-supervised
+# service. This is the canonical s6-overlay pattern for "container
+# exits when the program exits" semantics, and it lets us preserve
+# every pre-s6 invocation contract (chat passthrough, sleep infinity,
+# bash, --tui) without re-implementing argument routing through
+# /run/s6/container_environment.
+#
+# So why does this service exist at all? Two reasons:
+#   1. s6-rc requires at least one user service for the "user" bundle
+#      to be valid. We can't ship an empty bundle.
+#   2. Future work may want to supervise a long-lived hermes process
+#      (e.g. for gateway-server containers); having the slot already
+#      wired in keeps that change small.
+#
+# For now this service is a no-op: it sleeps forever, doing nothing.
+# The dashboard runs as a real s6 service alongside it (see
+# ../dashboard/run) and per-profile gateways register dynamically via
+# /run/service/ at runtime (Phase 4).
+exec sleep infinity

docker/s6-rc.d/main-hermes/type

@@ -0,0 +1 @@
+longrun

docker/stage2-hook.sh

@@ -0,0 +1,105 @@
+#!/bin/sh
+# s6-overlay stage2 hook — runs as root after the supervision tree is
+# up but before user services start. Handles UID/GID remap, volume
+# chown, config seeding, and skills sync.
+#
+# Per-service privilege drop happens inside each service's `run` script
+# (and in main-wrapper.sh) via s6-setuidgid, not here.
+#
+# Wired into the image as /etc/cont-init.d/01-hermes-setup by the
+# Dockerfile. The shim at docker/entrypoint.sh forwards to this script
+# so external references to docker/entrypoint.sh still work.
+#
+# NB: cont-init.d scripts run with no arguments — the user's CMD args
+# are NOT visible here. That's fine: we use Architecture B (s6-overlay
+# main-program model), so main-wrapper.sh runs the CMD with full
+# stdin/stdout/stderr access and handles arg parsing there.
+
+set -eu
+
+HERMES_HOME="${HERMES_HOME:-/opt/data}"
+INSTALL_DIR="/opt/hermes"
+
+# --- UID/GID remap ---
+if [ -n "${HERMES_UID:-}" ] && [ "$HERMES_UID" != "$(id -u hermes)" ]; then
+    echo "[stage2] Changing hermes UID to $HERMES_UID"
+    usermod -u "$HERMES_UID" hermes
+fi
+if [ -n "${HERMES_GID:-}" ] && [ "$HERMES_GID" != "$(id -g hermes)" ]; then
+    echo "[stage2] Changing hermes GID to $HERMES_GID"
+    # -o allows non-unique GID (e.g. macOS GID 20 "staff" may already
+    # exist as "dialout" in the Debian-based container image).
+    groupmod -o -g "$HERMES_GID" hermes 2>/dev/null || true
+fi
+
+# --- Fix ownership of data volume ---
+actual_hermes_uid=$(id -u hermes)
+needs_chown=false
+if [ -n "${HERMES_UID:-}" ] && [ "$HERMES_UID" != "10000" ]; then
+    needs_chown=true
+elif [ "$(stat -c %u "$HERMES_HOME" 2>/dev/null)" != "$actual_hermes_uid" ]; then
+    needs_chown=true
+fi
+if [ "$needs_chown" = true ]; then
+    echo "[stage2] Fixing ownership of $HERMES_HOME to hermes ($actual_hermes_uid)"
+    # In rootless Podman the container's "root" is mapped to an
+    # unprivileged host UID — chown will fail. That's fine: the volume
+    # is already owned by the mapped user on the host side.
+    chown -R hermes:hermes "$HERMES_HOME" 2>/dev/null || \
+        echo "[stage2] Warning: chown failed (rootless container?) — continuing"
+    # The .venv must also be re-chowned when UID is remapped, otherwise
+    # lazy_deps.py cannot install platform packages (discord.py, etc.).
+    chown -R hermes:hermes "$INSTALL_DIR/.venv" 2>/dev/null || \
+        echo "[stage2] Warning: chown .venv failed (rootless container?) — continuing"
+fi
+
+# --- config.yaml permissions ---
+# Ensure config.yaml is readable by the hermes runtime user even if it
+# was edited on the host after initial ownership setup.
+if [ -f "$HERMES_HOME/config.yaml" ]; then
+    chown hermes:hermes "$HERMES_HOME/config.yaml" 2>/dev/null || true
+    chmod 640 "$HERMES_HOME/config.yaml" 2>/dev/null || true
+fi
+
+# --- Seed directory structure as hermes user ---
+# Run as hermes via s6-setuidgid so dirs end up owned correctly (matters
+# under rootless Podman where chown back to root would fail).
+s6-setuidgid hermes sh -c "mkdir -p \"$HERMES_HOME\"/cron \
+    \"$HERMES_HOME\"/sessions \"$HERMES_HOME\"/logs \"$HERMES_HOME\"/hooks \
+    \"$HERMES_HOME\"/memories \"$HERMES_HOME\"/skills \"$HERMES_HOME\"/skins \
+    \"$HERMES_HOME\"/plans \"$HERMES_HOME\"/workspace \"$HERMES_HOME\"/home"
+
+# --- Install-method stamp (read by detect_install_method() in hermes status) ---
+# Preserved from the tini-era entrypoint (PR #27843). Must be written as
+# the hermes user so ownership matches the file's documented owner.
+s6-setuidgid hermes sh -c "echo docker > \"$HERMES_HOME/.install_method\"" 2>/dev/null || true
+
+# --- Seed config files (only on first boot) ---
+seed_one() {
+    dest=$1
+    src=$2
+    if [ ! -f "$HERMES_HOME/$dest" ] && [ -f "$INSTALL_DIR/$src" ]; then
+        s6-setuidgid hermes cp "$INSTALL_DIR/$src" "$HERMES_HOME/$dest"
+    fi
+}
+seed_one ".env" ".env.example"
+seed_one "config.yaml" "cli-config.yaml.example"
+seed_one "SOUL.md" "docker/SOUL.md"
+
+# auth.json: bootstrap from env on first boot only. Same semantics as the
+# pre-s6 entrypoint — the [ ! -f ] guard is critical to avoid clobbering
+# rotated refresh tokens on container restart.
+if [ ! -f "$HERMES_HOME/auth.json" ] && [ -n "${HERMES_AUTH_JSON_BOOTSTRAP:-}" ]; then
+    printf '%s' "$HERMES_AUTH_JSON_BOOTSTRAP" > "$HERMES_HOME/auth.json"
+    chown hermes:hermes "$HERMES_HOME/auth.json" 2>/dev/null || true
+    chmod 600 "$HERMES_HOME/auth.json"
+fi
+
+# --- Sync bundled skills ---
+if [ -d "$INSTALL_DIR/skills" ]; then
+    s6-setuidgid hermes sh -c \
+        ". $INSTALL_DIR/.venv/bin/activate && python3 $INSTALL_DIR/tools/skills_sync.py" \
+        || echo "[stage2] Warning: skills_sync.py failed; continuing"
+fi
+
+echo "[stage2] Setup complete; starting user services"

tests/docker/test_dashboard.py

@@ -92,3 +92,67 @@ def test_dashboard_port_override(
         deadline_s=60.0,
     )
     assert ok, f"Dashboard not listening on port 9120: stdout={stdout!r}"
+
+
+def test_dashboard_restarts_after_crash(
+    built_image: str, container_name: str,
+) -> None:
+    """Phase 2 invariant: under s6 supervision, killing the dashboard
+    process should be recovered automatically.
+
+    Pre-s6 (tini) behavior was "stays dead" — the test wouldn't have
+    passed against that image. After the s6-overlay migration the
+    dashboard runs as a longrun s6-rc service and s6-supervise restarts
+    it after a ~1s backoff (the default).
+    """
+    subprocess.run(
+        ["docker", "run", "-d", "--name", container_name,
+         "-e", "HERMES_DASHBOARD=1", built_image, "sleep", "120"],
+        check=True, capture_output=True, timeout=30,
+    )
+    # Wait for the first dashboard to come up.
+    ok, _ = _poll(
+        container_name, "pgrep -f 'hermes dashboard'", deadline_s=30.0,
+    )
+    assert ok, "Dashboard never started initially"
+
+    # Grab the initial PID. s6 may briefly transition through restart
+    # state between our poll-success and the follow-up pgrep, so retry
+    # a couple of times before giving up.
+    first_pid: str | None = None
+    for _attempt in range(10):
+        first_pid_result = subprocess.run(
+            ["docker", "exec", container_name,
+             "pgrep", "-f", "hermes dashboard"],
+            capture_output=True, text=True, timeout=10,
+        )
+        first_pids = first_pid_result.stdout.strip().split()
+        if first_pids:
+            first_pid = first_pids[0]
+            break
+        time.sleep(0.5)
+    assert first_pid is not None, "Could not capture initial dashboard PID"
+
+    # Kill the dashboard.
+    subprocess.run(
+        ["docker", "exec", container_name, "kill", "-9", first_pid],
+        capture_output=True, timeout=10,
+    )
+
+    # s6 backs off ~1s before restart; allow up to 15s for the new
+    # process to appear with a different PID.
+    deadline = time.monotonic() + 15.0
+    while time.monotonic() < deadline:
+        r = subprocess.run(
+            ["docker", "exec", container_name,
+             "pgrep", "-f", "hermes dashboard"],
+            capture_output=True, text=True, timeout=10,
+        )
+        pids = r.stdout.strip().split() if r.returncode == 0 else []
+        if pids and pids[0] != first_pid:
+            return  # success
+        time.sleep(0.5)
+
+    raise AssertionError(
+        f"Dashboard not restarted after kill (first_pid={first_pid})"
+    )