fre make container build needs exec script in second stage

[thomas-robinson]

Describe the bug
The two stage container build in fre make needs to copy over the execution script from the first stage and set up a symbolic link in the second stage. Here is an example of what the Dockerfile should look like for ESM

COPY --from=builder /apps/esm4.5_om5b08_compile_v6_cobv3_mekep/exec /apps/esm4.5_om5b08_compile_v6_cobv3_mekep/exec
RUN mkdir -p /apps/bin \
 && ln -sf /apps/esm4.5_om5b08_compile_v6_cobv3_mekep/exec/execrunscript.sh /apps/bin/execrunscript.sh

This can be done by modifying fre make to add in the link set up line in the second stage of the Dockerfile.

Additionally, the LD_LIBRARY_PATH of the container is being overwritten in frerun. frerun needs to be patched to allow for the LD_LIBRARY_PATH of the container to be appended on to the end of the APPTAINER_LD_LIBRARY_PATH. It's currently set up like this:
setenv APPTAINERENV_LD_LIBRARY_PATH "${CRAY_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}:/opt/cray/pe/lib64:/usr/lib64/libibverbs:/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pals/1.4/lib"
It needs to have no quotes " and have :\$LD_LIBRARY_PATH added to the end. Final should be:
setenv APPTAINERENV_LD_LIBRARY_PATH ${CRAY_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}:/opt/cray/pe/lib64:/usr/lib64/libibverbs:/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pals/1.4/lib:\$LD_LIBRARY_PATH @rem1776

To Reproduce

Expected behavior
The model running

Additional context
Tom will do fre make. Ryan may need to do frerun.