Delete empty directories after pulling ground truth

Because object stores don't actually have directories, when we
rsync, looks like sometimes empty directories are left behind. It
makes the zarr a bit weird if 'directories' are renamed.

We could 'fix' this by pulling the entire zarr file each time,
but that's unnecessarily going to slow things down. Instead, we
delete all empty directories

helm-charts/app/common.values.yaml

@@ -21,13 +21,15 @@ frx-challenges:
         - /bin/sh
         - -c
         # use printf so we don't interpret the \n in service account keys's private key
+        # Delete empty directories, since `gcloud storage rsync` with `--delete-unmatched-destination-objects`
+        # does not seem to actually delete directories created, only the leaf objects (sometimes).
         - |
           export CLOUDSDK_AUTH_CREDENTIAL_FILE_OVERRIDE=/tmp/gcloud-auth && \
           printf '%s' "$SERVICE_ACCOUNT_JSON_KEY" > $CLOUDSDK_AUTH_CREDENTIAL_FILE_OVERRIDE && \
-          cat $CLOUDSDK_AUTH_CREDENTIAL_FILE_OVERRIDE && \
           mkdir -p /opt/state/truth/ && \
           gcloud storage rsync --recursive --delete-unmatched-destination-objects \
-            gs://cellmap-challenge-ground-truth-fake/gt.zarr /opt/state/truth/gt.zarr
+            gs://cellmap-challenge-ground-truth-fake/gt.zarr /opt/state/truth/gt.zarr && \
+          find /opt/state/truth/ -type d -empty -delete
       volumeMounts:
         - name: storage
           mountPath: /opt/state