feat: enhance Docker setup with entrypoint script and skill management

- Added a new entrypoint script to manage ownership of bind-mounted directories and merge built-in skills into preloaded ones.
- Updated the Dockerfile to include the `gosu` package for privilege management and to set the entrypoint to the new script.
- Ensured built-in skills are preserved and accessible after bind-mounting user directories, improving the application's flexibility and usability.

These changes streamline the container initialization process and enhance the management of skills within the application.

docker/Dockerfile.app

@@ -65,7 +65,8 @@ RUN if [ -n "$APK_MIRROR_ARG" ]; then \
         build-essential postgresql-client default-mysql-client ca-certificates tzdata sed curl bash vim wget \
         libsqlite3-0 \
         python3 python3-pip python3-dev libffi-dev libssl-dev \
-        nodejs npm && \
+        nodejs npm \
+        gosu && \
     python3 -m pip install --break-system-packages --upgrade pip setuptools wheel && \
     mkdir -p /home/appuser/.local/bin && \
     curl -LsSf https://astral.sh/uv/install.sh | CARGO_HOME=/home/appuser/.cargo UV_INSTALL_DIR=/home/appuser/.local/bin sh && \
@@ -89,16 +90,20 @@ COPY --from=builder /app/scripts ./scripts
 COPY --from=builder /app/migrations ./migrations
 COPY --from=builder /app/dataset/samples ./dataset/samples
 COPY --from=builder /app/skills/preloaded ./skills/preloaded
+# Keep a read-only backup so bind-mount cannot erase built-in skills
+COPY --from=builder /app/skills/preloaded ./skills/_builtin
 COPY --from=builder /root/.duckdb /home/appuser/.duckdb
 COPY --from=builder /app/WeKnora .
 
+# Copy and make entrypoint script executable
+COPY --from=builder /app/scripts/docker-entrypoint.sh ./scripts/docker-entrypoint.sh
+
 # Make scripts executable
 RUN chmod +x ./scripts/*.sh
 
 # Expose ports
 EXPOSE 8080
 
-# Switch to non-root user and run the application directly
-USER appuser
 
+ENTRYPOINT ["./scripts/docker-entrypoint.sh"]
 CMD ["./WeKnora"]

scripts/docker-entrypoint.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+set -e
+
+# ─── Fix ownership of bind-mounted directories ───
+# When users bind-mount host directories (e.g. ./skills/preloaded),
+# the mount inherits the host UID/GID which may differ from the
+# container's appuser. This entrypoint runs as root, fixes ownership,
+# then drops privileges to appuser via gosu — the same pattern used
+# by official postgres/redis images.
+
+# Directories that may be bind-mounted and need appuser access
+MOUNT_DIRS=(
+    /app/skills/preloaded
+    /data/files
+)
+
+for dir in "${MOUNT_DIRS[@]}"; do
+    if [ -d "$dir" ]; then
+        chown -R appuser:appuser "$dir" 2>/dev/null || true
+    fi
+done
+
+# ─── Merge built-in skills into preloaded ───
+# Built-in skills are backed up at /app/skills/_builtin during image build.
+# After a bind-mount replaces /app/skills/preloaded, copy back any
+# missing built-in skills (without overwriting user-provided ones).
+BUILTIN_DIR="/app/skills/_builtin"
+PRELOADED_DIR="/app/skills/preloaded"
+
+if [ -d "$BUILTIN_DIR" ]; then
+    mkdir -p "$PRELOADED_DIR"
+    for skill_dir in "$BUILTIN_DIR"/*/; do
+        [ -d "$skill_dir" ] || continue
+        skill_name="$(basename "$skill_dir")"
+        if [ ! -d "$PRELOADED_DIR/$skill_name" ]; then
+            cp -r "$skill_dir" "$PRELOADED_DIR/$skill_name"
+        fi
+    done
+    chown -R appuser:appuser "$PRELOADED_DIR"
+fi
+
+# ─── Drop privileges and exec the main process ───
+exec gosu appuser "$@"