Move entrypoint.sh out of docker/ directory

Dockerfile

@@ -5,19 +5,19 @@ FROM rocker/r-ver:latest
 #   Single RUN directive and two COPY directives
 #     Pre-RUN COPY for relatively stable files, post-RUN COPY for app files
 #   Avoid other directives like USER and ENV
-#     entrypoint.sh activates the virtual environment for running the app
+#     startup.sh activates the virtual environment for running the app
 # Considerations for remote development (HF Spaces Dev Mode)
 #   Dev Mode requires useradd, chown and USER
 #   Use CMD instead of ENTRYPOINT
 
 # Set working directory and copy non-app files
 WORKDIR /app
-COPY requirements.txt docker/entrypoint.sh .
+COPY requirements.txt entrypoint.sh .
 
 # Install Python and system tools
 # Create and activate virtual environment for installing packages
 # Install required Python and R packages
-# Make startup script executable
+# Rename startup script and make it executable
 # Add user with uid=1000 and chown /app directory for HF Spaces Dev Mode
 RUN apt-get update && \
     apt-get install -y python3 python3-pip python3-venv screen vim git && \
@@ -27,17 +27,18 @@ RUN apt-get update && \
     export PATH="/opt/venv/bin:$PATH" && \
     pip --no-cache-dir install -r requirements.txt && \
     R -q -e 'install.packages(c("ellmer", "mcptools", "readr", "ggplot2", "tidyverse"))' && \
-    chmod +x entrypoint.sh && \
+    cp entrypoint.sh startup.sh && \
+    chmod +x startup.sh && \
     useradd -m -u 1000 user && \
     chown -R user /app
     
 # Copy app files with user permissions
-# NOTE: because the repo has docker/entrypoint.sh, this does *not*
-# overwrite the entrypoint.sh that we made executable above
+# NOTE: This overwrites all copied files, rendering them non-executable. That is why we
+# created an executable file with a different name (startup.sh) that is not overwritten here.
 COPY --chown=user . /app
 
 # Set the user for Dev Mode
 USER user
 
 # Set default command (executable file in WORKDIR)
-CMD [ "/app/entrypoint.sh" ]
+CMD [ "/app/startup.sh" ]