diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2d4bf65..3da7191 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -26,11 +26,7 @@ jobs:
   test-pathogen-repo-ci:
     uses: ./.github/workflows/pathogen-repo-ci.yaml
     with:
-      # XXX TODO: Revert back to nextstrain/zika (for consistency with
-      # elsewhere) once pathogen-repo-ci has support for running workflows in
-      # subdirs (i.e. for our new repo layout).
-      #   -trs, 30 Jan 2024
-      repo: nextstrain/ebola
+      repo: nextstrain/zika
       artifact-name: outputs-test-pathogen-repo-ci
     secrets: inherit
 
diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index d4a9f9e..71149f9 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -3,6 +3,15 @@
 # workflow) in this repo for an example of what the caller workflow looks like.
 name: CI
 
+defaults:
+  run:
+    # This is the same as GitHub Action's `bash` keyword as of 20 June 2023:
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell
+    #
+    # Completely spelling it out here so that GitHub can't change it out from under us
+    # and we don't have to refer to the docs to know the expected behavior.
+    shell: bash --noprofile --norc -eo pipefail {0}
+
 on:
   workflow_call:
     inputs:
@@ -65,15 +74,20 @@ on:
 
       artifact-name:
         description: >-
-          Name to use for build results artifact uploaded at the end of the
-          workflow.  This name will be suffixed with other information from the
-          workflow job matrix to distinguish each artifact in a workflow run.
+          A base name to use for the uploaded artifacts from the
+          build. This will be concatenated with the directory name
+          used to invoke the build to generate the full artifact file
+          name.
+
+          Defaults to `ci-outputs`.
 
-          If you're invoking this workflow multiple times from the same calling
-          workflow, you should set this.  Otherwise, the default of "outputs"
-          is probably fine.
+          N.b., you almost certainly don't need to change this, unless
+          you're running multiple invocations of this action in a
+          single workflow. Then you should provide unique values to
+          ensure you can access the artifacts from all the builds
+          you're doing.
         type: string
-        default: outputs
+        default: ci-outputs
         required: false
 
       continue-on-error:
@@ -85,8 +99,12 @@ on:
 
 permissions:
   contents: read
+  id-token: write
   packages: read
 
+env:
+  NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
+
 jobs:
   configuration:
     runs-on: ubuntu-latest
@@ -101,8 +119,17 @@ jobs:
     outputs:
       runtimes: ${{ steps.inputs.outputs.runtimes }}
 
-  build:
-    needs: configuration
+  workflow-context:
+    runs-on: ubuntu-latest
+    steps:
+      - id: workflow-context
+        uses: nextstrain/.github/actions/workflow-context@master
+    outputs:
+      repository: ${{ steps.workflow-context.outputs.repository }}
+      sha: ${{ steps.workflow-context.outputs.sha }}
+
+  nextstrain-build:
+    needs: [configuration, workflow-context]
     strategy:
       fail-fast: false
       matrix:
@@ -196,58 +223,44 @@ jobs:
           '
           | tee -a "$GITHUB_ENV"
 
-      - uses: actions/checkout@v4
+      - name: Checkout ${{ inputs.repo }}
+        uses: actions/checkout@v4
         with:
           repository: ${{ inputs.repo }}
 
-      # XXX TODO: It would be better for this to call setup-nextstrain-cli
-      # using the same ref that this workflow was called with (e.g. if this
-      # workflow was invoked by the caller workflow with @foo than we invoke
-      # the action with @foo too), but it's not currently possible to figure
-      # out that ref.  See discussion around this (including results of some
-      # investigation I did):
-      #
-      #   - https://github.community/t/reusable-workflows-get-the-ref-inside-the-called-workflow/224109
-      #   - https://github.community/t/ref-head-in-reusable-workflows/203690/92
-      #
-      # Once we can figure out that ref, then we can actions/checkout our
-      # nextstrain/.github repo at that ref as a sidecar path somewhere and
-      # then invoke the setup-nextstrain-cli action using a local file path
-      # instead of a remote owner/repo path.  This separate checkout will be
-      # necessary since the "uses:" key can't be interpolated (${{…}}) with
-      # context vars.
-      #
-      # For now, update the hardcoded ref (e.g. @90af34…) below when you make
-      # future changes to setup-nextstrain-cli.
-      #
-      # [ Update 16 Feb 2024: We solved this for pathogen-repo-build.yaml, but
-      #   because it required a new permission on the GitHub tokens (id-token:
-      #   write) we decided not to update this workflow (yet?) to use the same
-      #   approach. -trs ]
-      #
-      #   -trs, 28 April 2022
-      - uses: nextstrain/.github/actions/setup-nextstrain-cli@c1191de9d5e1a30e91d70b0fd1041d97ed1b2496
+      # Need to run this after the build repo is cloned so that cloning the
+      # build repo does not overwrite the .git dir and remove the extra support files
+      # that we need from nextstrain/.github repo
+      - name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
+        uses: actions/checkout@v4
         with:
+          repository: ${{ needs.workflow-context.outputs.repository }}
+          ref: ${{ needs.workflow-context.outputs.sha }}
+          path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
+
+      - name: Set up Nextstrain runtime ${{ matrix.runtime }}
+        uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
+        with:
+          cli-version: ">=8.3.0"
           runtime: ${{ matrix.runtime }}
 
-      - name: Copy example data
-        run: |
-          if [[ -d example_data ]]; then
-            mkdir -p data/
-            cp -r -v example_data/* data/
-          else
-            echo No example data to copy.
-          fi
+      - name: Run ingest
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
+        with:
+          directory: ingest
+          runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
 
-      - run: nextstrain build . ${{ inputs.build-args }}
+      - name: Run phylogenetic
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
+        with:
+          directory: phylogenetic
+          runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
 
-      - if: always()
-        uses: actions/upload-artifact@v4
+      - name: Run nextclade
+        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
-          path: |
-            auspice/
-            results/
-            benchmarks/
-            logs/
-            .snakemake/log/
+          directory: nextclade
+          runtime: ${{ matrix.runtime }}
+          artifact-name: ${{ inputs.artifact-name }}
diff --git a/README.md b/README.md
index 261e48e..b9a506a 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,7 @@ See also GitHub's [documentation on issue and PR templates](https://docs.github.
 
 Invoked by our GitHub Actions workflows, including the reusable workflows below.
 
+- [Run Nextstrain CI Build](actions/run-nextstrain-ci-build/action.yaml)
 - [Setup Nextstrain CLI](actions/setup-nextstrain-cli/action.yaml)
 - [shellcheck](actions/shellcheck/action.yaml)
 - [Setup SSH](actions/setup-ssh/action.yaml) access to runner machine
diff --git a/actions/run-nextstrain-ci-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
new file mode 100644
index 0000000..66cf141
--- /dev/null
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -0,0 +1,58 @@
+name: run-nextstrain-ci-build
+description: >-
+  Runs a single `nextstrain build` command in a given sub-directory of
+  a pathogen repo. Must be provided with the name of the sub-directory
+  and the runtime to use. Requires that the Nextstrain CLI runtime
+  already be provisioned (e.g., via the `setup-nextstrain-cli` action
+  in this repo).
+
+  Note that this action exists primarily as a means to keep the
+  `pathogen-repo-ci` workflow DRY; it is unlikely to be useful outside
+  the context of that specific workflow.
+
+inputs:
+  artifact-name:
+    description: >-
+      Name to append to the build directory to generate a
+      unique artifact name for the upload action.
+    type: string
+    required: true
+  directory:
+    description: The name of the sub-directory to run the build from
+    type: string
+    required: true
+  runtime:
+    description: Nextstrain runtime to use for the build
+    type: string
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - id: run-build
+      env:
+        DIR: ${{ inputs.directory }}
+      run: |
+        if [[ -f nextstrain-pathogen.yaml && -f "$DIR"/Snakefile && -f "$DIR"/build-configs/ci/config.yaml ]]; then
+          nextstrain check-setup ${{ inputs.runtime }} --set-default
+          nextstrain build "$DIR" --configfile build-configs/ci/config.yaml
+        else
+          echo "Skipping $DIR build due to one or more missing files."
+          for i in nextstrain-pathogen.yaml "$DIR"/Snakefile "$DIR"/build-configs/ci/config.yaml; do
+            [[ -f $i ]] || echo missing $i
+          done
+        fi
+      shell: bash
+
+    - id: upload-artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ inputs.artifact-name }}-${{ inputs.directory }}-${{ inputs.runtime }}
+        if-no-files-found: ignore
+        path: |
+          ${{ inputs.directory }}/.snakemake/log/
+          ${{ inputs.directory }}/auspice/
+          ${{ inputs.directory }}/benchmarks/
+          ${{ inputs.directory }}/logs/
+          ${{ inputs.directory }}/results/
diff --git a/actions/setup-nextstrain-cli/action.yaml b/actions/setup-nextstrain-cli/action.yaml
index ace540a..be6db12 100644
--- a/actions/setup-nextstrain-cli/action.yaml
+++ b/actions/setup-nextstrain-cli/action.yaml
@@ -1,7 +1,3 @@
-# If you update this action, please update the hardcoded ref to it in
-# .github/workflows/pathogen-repo-ci.yaml.  See the commentary there for why
-# it's necessary.
-
 name: Setup Nextstrain CLI
 description: >-
   This GitHub Actions action is intended to be called by workflows in our other