Appending the same environment variable in different places yields incorrect export results

[dqwu]

In my E3SM feature branch, config_machines.xml appends PKG_CONFIG_PATH in two places on the machine frontier:

<environment_variables>
  <env name="PKG_CONFIG_PATH">$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}</env>
  ...
</environment_variables>
...
<environment_variables compiler="gnu.*" mpilib="mpich">
  ...
  <env name="PKG_CONFIG_PATH">/lustre/orion/cli115/world-shared/frontier/3rdparty/protobuf/21.6/gcc-12.2.0/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}</env>
</environment_variables>

After running case.setup, .env_mach_specific.sh shows:

export PKG_CONFIG_PATH=/opt/cray/pe/libsci/23.09.1.1/GNU/10.3/x86_64/lib/pkgconfig:/lustre/orion/cli115/world-shared/frontier/3rdparty/protobuf/21.6/gcc-12.2.0/lib/pkgconfig:/opt/cray/pe/parallel-netcdf/1.12.3.1/gnu/9.1/lib/pkgconfig:/opt/cray/pe/netcdf-hdf5parallel/4.9.0.1/gnu/9.1/lib/pkgconfig:/opt/cray/pe/hdf5-parallel/1.12.2.1/gnu/9.1/lib/pkgconfig:/opt/cray/libfabric/1.15.2.0/lib64/pkgconfig:/sw/frontier/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-zuyclcfig4tizmb2bm2h4roqsp3rwn2y/lib/pkgconfig:/sw/frontier/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/subversion-1.14.1-rcptsltz4q4clvbt5e2aua25nvwdf4ss/share/pkgconfig:/opt/cray/pe/gcc/12.2.0/snos/lib/pkgconfig:/opt/cray/pe/dsmml/0.2.2/dsmml/lib/pkgconfig:/opt/cray/pe/craype/2.7.31.11/pkg-config:/opt/cray/pe/pmi/6.1.13/lib/pkgconfig
...
export PKG_CONFIG_PATH=/lustre/orion/cli115/world-shared/frontier/3rdparty/protobuf/21.6/gcc-12.2.0/lib/pkgconfig:/lustre/orion/cli115/world-shared/frontier/3rdparty/protobuf/21.6/gcc-12.2.0/lib/pkgconfig:/opt/cray/pe/parallel-netcdf/1.12.3.1/gnu/9.1/lib/pkgconfig:/opt/cray/pe/netcdf-hdf5parallel/4.9.0.1/gnu/9.1/lib/pkgconfig:/opt/cray/pe/hdf5-parallel/1.12.2.1/gnu/9.1/lib/pkgconfig:/opt/cray/libfabric/1.15.2.0/lib64/pkgconfig:/sw/frontier/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-zuyclcfig4tizmb2bm2h4roqsp3rwn2y/lib/pkgconfig:/sw/frontier/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/subversion-1.14.1-rcptsltz4q4clvbt5e2aua25nvwdf4ss/share/pkgconfig:/opt/cray/pe/gcc/12.2.0/snos/lib/pkgconfig:/opt/cray/pe/dsmml/0.2.2/dsmml/lib/pkgconfig:/opt/cray/pe/craype/2.7.31.11/pkg-config:/opt/cray/pe/pmi/6.1.13/lib/pkgconfig

For the second "export PKG_CONFIG_PATH=XXXX" call in .env_mach_specific.sh, /opt/cray/pe/libsci/23.09.1.1/GNU/10.3/x86_64/lib/pkgconfig (in the first call) is lost.

Steps to reproduce:

[Clone the E3SM repository]

git clone https://github.com/E3SM-Project/E3SM.git
cd E3SM

git merge --no-edit origin/dqwu/machinefiles/adios-upgrade
git submodule update --init

[Create and set up a simple X case]

cd cime/scripts

./create_newcase --machine=frontier --compiler=gnu --case X_f19_g16 --compset X --res f19_g16

cd X_f19_g16

./case.setup

[Check .env_mach_specific.sh]
cat .env_mach_specific.sh

[jedwards4b]

@dqwu I think that supporting the feature you are requesting would be quite complicated. You could simply repeat the first change to PKG_CONFIG_PATH in the second as:
<env name="PKG_CONFIG_PATH">/lustre/orion/cli115/world-shared/frontier/3rdparty/protobuf/21.6/gcc-12.2.0/lib/pkgconfig:$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}</env>