don't directly overwrite spack.yaml (breaks spack command)

.gitlab-ci.yml

@@ -199,7 +199,8 @@ build-spack-env-on-runner:
     - spack env create $SPACK_DEV_ENV
     - spack env activate $SPACK_DEV_ENV
     - rm -rf $SPACK_ENV/site-config && cp -r site-config $SPACK_ENV
-    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > $SPACK_ENV/spack.yaml
+    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+    - cp /tmp/spack.yaml $SPACK_ENV/
     - spack install -y -j2 --fresh --test root
   after_script:
     - mkdir spack_logs
@@ -274,7 +275,8 @@ sync-gitlab-spack-instance:
     # update environment site-configs
     - rm -rf $SPACK_ENV/site-config && cp -r site-config $SPACK_ENV
     # update spack.yaml: merge top-level and site-specific spack.yaml files
-    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > $SPACK_ENV/spack.yaml
+    - spack-python site-config/ymerge.py spack.yaml site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+    - cp /tmp/spack.yaml $SPACK_ENV/
     # There is a known spack bug (https://github.com/spack/spack/issues/29447) in installing test dependencies for installation tests. The workaround suggested
     # in the issue is to NOT concretize separately, but simply remove the .lock file and let the enironment be concretized by the spack install command:
     - rm $SPACK_ROOT/var/spack/environments/$SPACK_NFS_ENV/spack.lock || echo "No spack.lock file"

install_spack_env.sh

@@ -59,7 +59,8 @@ rm -rf $SPACK_ENV/site-config && cp -r $EBRAINS_REPO/site-config $SPACK_ENV
 # update spack.yaml: merge top-level and site-specific spack.yaml files
 # TODO: find a more robust way to do this (maybe with yq? but we need to download the binary)
 # TODO: or add pyyaml to dependencies and use python script
-spack-python $EBRAINS_REPO/site-config/ymerge.py $EBRAINS_REPO/spack.yaml $EBRAINS_REPO/site-config/$SYSTEMNAME/spack.yaml > $SPACK_ENV/spack.yaml
+spack-python $EBRAINS_REPO/site-config/ymerge.py $EBRAINS_REPO/spack.yaml $EBRAINS_REPO/site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
+cp /tmp/spack.yaml $SPACK_ENV/
 
 # There is a known spack bug (https://github.com/spack/spack/issues/29447) in installing test dependencies
 # for installation tests. The workaround suggested in the issue is to NOT concretize separately, but simply