Remove set-branch-ingest-config

Recently learned that Snakemake no longer overwrites the entire config
when providing nested config values via the `--config` option.¹ This
allows us to remove the set-branch-ingest-config script and directly set
branch config values via the command line option in our GitHub Action
workflows.

I've opted to use `jq` to interpolate the branch name into the S3_DST
because I didn't want to fiddle with escaping quotes in the JSON string.

¹ nextstrain/dengue#13 (comment)

.github/workflows/fetch-and-ingest-branch.yaml

@@ -26,11 +26,10 @@ jobs:
 
       - name: run_pipeline
         run: |
+          # Create JSON string for the nested upload config
           GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
-          ./phylogenetic/bin/set-branch-ingest-config \
-            --config-yaml ingest/config/optional.yaml \
-            --s3-dst s3://nextstrain-data/files/workflows/monkeypox/branch/"${GITHUB_BRANCH}" \
-            > ingest/config/optional-branch.yaml
+          S3_DST="s3://nextstrain-data/files/workflows/monkeypox/branch/${GITHUB_BRANCH}"
+          UPLOAD_CONFIG=$(jq -n --arg S3_DST "$S3_DST" '{"s3": {"dst": $S3_DST }}')
 
           nextstrain build \
             --aws-batch \
@@ -43,8 +42,8 @@ jobs:
             --env AWS_SECRET_ACCESS_KEY \
             --env GITHUB_RUN_ID \
             ingest \
-              --configfiles config/config.yaml config/optional-branch.yaml \
-              --config trigger_rebuild=False
+              --configfiles config/config.yaml config/optional.yaml \
+              --config trigger_rebuild=False send_slack_notifications=False upload="$UPLOAD_CONFIG"
         env:
           AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}