Update Dockerfile to create necessary directories

Dockerfile

@@ -30,6 +30,9 @@ ENV HOME=/home/user \
     PATH=/home/user/.local/bin:$PATH \
     PYTHONPATH=/app
 
+# Create necessary directories
+RUN mkdir -p ./figures ./pdfs ./src/processed_markdown
+
 # Copy and install Python requirements
 COPY --chown=user requirements.txt .
 RUN pip install --no-cache-dir -r requirements.txt
@@ -39,10 +42,8 @@ COPY --chown=user --from=frontend-builder /app/frontend/.next ./.next
 COPY --chown=user --from=frontend-builder /app/frontend/public ./public
 COPY --chown=user --from=frontend-builder /app/frontend/package*.json ./
 
-# Copy backend code and other necessary files
+# Copy backend code
 COPY --chown=user src/ ./src/
-COPY --chown=user figures/ ./figures/
-COPY --chown=user pdfs/ ./pdfs/
 
 # Install frontend production dependencies
 RUN npm install --production