fix: address permission and .env issues

Dockerfile

@@ -15,6 +15,9 @@ RUN apt-get update && apt-get install -y \
 # Create directories
 RUN mkdir -p /app/dependencies /app/data/sqlite /app/data/chroma_db /app/logs /app/run /app/resources
 
+# Set permissions for writable directories
+RUN chmod -R 777 /app/data /app/logs /app/run /app/resources
+
 # Copy dependency files - Files that rarely change
 COPY dependencies/graphrag-1.2.1.dev27.tar.gz /app/dependencies/
 COPY dependencies/llama.cpp.zip /app/dependencies/
@@ -61,6 +64,9 @@ RUN echo "--- Listing /app/lpm_kernel directory ---" && ls -la /app/lpm_kernel
 # Copy the start script
 COPY start.sh /app/
 
+# Copy .env file
+COPY .env /app/.env
+
 # Check module import
 RUN python -c "import lpm_kernel; print('Module import check passed')"
 
@@ -72,10 +78,11 @@ ENV PYTHONUNBUFFERED=1 \
     RUN_DIR=/app/run \
     RESOURCES_DIR=/app/resources \
     APP_ROOT=/app \
-    FLASK_APP=lpm_kernel.app
+    FLASK_APP=lpm_kernel.app \
+    TRANSFORMERS_CACHE=/app/.cache/huggingface
 
 # Expose ports
 EXPOSE 8002 8080
 
 # Set the startup command
-CMD ["./start.sh"]
+CMD ["./start.sh"]