Fix: no symlinks, chown /data/neo4j to neo4j user, direct console output to supervisord

Dockerfile

@@ -60,6 +60,9 @@ RUN { \
     echo "dbms.logs.query.enabled=OFF"; \
     echo "dbms.security.procedures.unrestricted=apoc.*"; \
     echo "dbms.security.procedures.allowlist=apoc.*"; \
+    echo "server.directories.data=/data/neo4j/data"; \
+    echo "server.directories.logs=/data/neo4j/logs"; \
+    echo "server.directories.run=/data/neo4j/run"; \
 } >> /etc/neo4j/neo4j.conf
 
 # ── Python backend ────────────────────────────────────────────────────────────

docker/entrypoint.sh

@@ -4,18 +4,8 @@ set -e
 log() { echo "[entrypoint] $*"; }
 
 # ── Persistent data dirs ───────────────────────────────────────────────────────
-mkdir -p /data/neo4j/data /data/neo4j/logs
-chown -R neo4j:neo4j /data/neo4j 2>/dev/null || true
-
-# Symlink Neo4j data/logs to persistent volume
-if [ ! -L /var/lib/neo4j/data ]; then
-    rm -rf /var/lib/neo4j/data
-    ln -sf /data/neo4j/data /var/lib/neo4j/data
-fi
-if [ ! -L /var/log/neo4j ]; then
-    rm -rf /var/log/neo4j
-    ln -sf /data/neo4j/logs /var/log/neo4j
-fi
+mkdir -p /data/neo4j/data /data/neo4j/logs /data/neo4j/run
+chown -R neo4j:neo4j /data/neo4j
 
 # ── First-boot: set initial password ──────────────────────────────────────────
 NEO4J_PASS="${NEO4J_PASSWORD:-clinicalmatch2024}"

docker/supervisord.conf

@@ -15,8 +15,8 @@ serverurl=unix:///tmp/supervisor.sock
 
 # ── Neo4j Community ────────────────────────────────────────────────────────────
 [program:neo4j]
-command=su -s /bin/bash neo4j -c "neo4j console >> /data/neo4j/logs/console.log 2>&1"
-environment=NEO4J_HOME=/var/lib/neo4j,NEO4J_CONF=/etc/neo4j
+command=su -s /bin/bash neo4j -c "NEO4J_CONF=/etc/neo4j neo4j console"
+environment=NEO4J_HOME=/var/lib/neo4j
 autostart=true
 autorestart=true
 startsecs=45