diff --git a/template.rb b/template.rb
index 8108998f..8844a655 100644
--- a/template.rb
+++ b/template.rb
@@ -112,7 +112,6 @@ def apply_template! # rubocop:disable Metrics/MethodLength, Metrics/AbcSize, Met
   apply "variants/backend-base/bin/template.rb"
   apply "variants/backend-base/config/template.rb"
   apply "variants/backend-base/doc/template.rb"
-  apply "variants/backend-base/lib/template.rb"
   apply "variants/backend-base/public/template.rb"
   apply "variants/backend-base/spec/template.rb"
 
@@ -122,6 +121,10 @@ def apply_template! # rubocop:disable Metrics/MethodLength, Metrics/AbcSize, Met
   after_bundle do
     require_package_json_gem
 
+    apply "variants/backend-base/lib/template.rb"
+
+    template "variants/backend-base/bin/setup.tt", "bin/setup", force: true
+
     # Remove the `test/` directory because we always use RSpec which creates
     # its own `spec/` directory
     remove_dir "test"
diff --git a/variants/backend-base/bin/setup b/variants/backend-base/bin/setup.tt
similarity index 95%
rename from variants/backend-base/bin/setup
rename to variants/backend-base/bin/setup.tt
index 566bfdf9..673aff49 100755
--- a/variants/backend-base/bin/setup
+++ b/variants/backend-base/bin/setup.tt
@@ -5,7 +5,7 @@ def setup!
     test "ruby -v" => ruby_version
     run  "gem install bundler --no-document --conservative"
     run  "bundle install"
-    run  "yarn install" if File.exist?("yarn.lock")
+    run  "<%= package_json.manager.native_install_command %>" if File.exist?("package.json")
     run  "bundle exec overcommit --install"
     copy "example.env"
     copy "config/secrets.example.yml"
diff --git a/variants/backend-base/lib/tasks/assets.rake b/variants/backend-base/lib/tasks/assets.rake.tt
similarity index 65%
rename from variants/backend-base/lib/tasks/assets.rake
rename to variants/backend-base/lib/tasks/assets.rake.tt
index cccebfef..684c525c 100644
--- a/variants/backend-base/lib/tasks/assets.rake
+++ b/variants/backend-base/lib/tasks/assets.rake.tt
@@ -1,7 +1,7 @@
 namespace :assets do
   desc "Ensures that dependencies required to compile assets are installed"
   task install_dependencies: :environment do
-    raise if File.exist?("yarn.lock") && !(system "yarn install --frozen-lockfile")
+    raise if File.exist?("package.json") && !(system "<%= package_json.manager.native_install_command(frozen: true) %>")
   end
 end
 
diff --git a/variants/backend-base/lib/template.rb b/variants/backend-base/lib/template.rb
index 6c68cef1..e8266478 100644
--- a/variants/backend-base/lib/template.rb
+++ b/variants/backend-base/lib/template.rb
@@ -1,4 +1,5 @@
 copy_file "variants/backend-base/lib/tasks/coverage.rake", "lib/tasks/coverage.rake"
-copy_file "variants/backend-base/lib/tasks/assets.rake", "lib/tasks/assets.rake"
 copy_file "variants/backend-base/lib/tasks/app.rake", "lib/tasks/app.rake"
 copy_file "variants/backend-base/lib/tasks/dev.rake", "lib/tasks/dev.rake"
+
+template "variants/backend-base/lib/tasks/assets.rake.tt", "lib/tasks/assets.rake", force: true
diff --git a/variants/frontend-base/template.rb b/variants/frontend-base/template.rb
index 938450f6..1a952ed9 100644
--- a/variants/frontend-base/template.rb
+++ b/variants/frontend-base/template.rb
@@ -13,7 +13,9 @@
 remove_dir "app/assets/stylesheets"
 remove_dir "app/assets/images"
 
-# this will create a package.json for us
+# shakapacker will create a more complete package.json
+remove_file "package.json"
+
 run "rails shakapacker:install"
 
 # this is added by shakapacker:install, but we've already got one (with some extra tags)
diff --git a/variants/github_actions_ci/workflows/ci.yml.tt b/variants/github_actions_ci/workflows/ci.yml.tt
index 4bbfabda..7ec9c7ff 100644
--- a/variants/github_actions_ci/workflows/ci.yml.tt
+++ b/variants/github_actions_ci/workflows/ci.yml.tt
@@ -47,12 +47,12 @@ jobs:
         with:
           node-version-file: ".node-version"
           cache: "yarn"
-      - run: yarn install --frozen-lockfile
+      - run: <%- package_json.manager.native_install_command(frozen: true) -%>
       <%- if TEMPLATE_CONFIG.use_typescript? -%>
-      - run: yarn run typecheck
+      - run: <%- package_json.manager.native_run_command("install") -%>
       <%- end -%>
-      - run: yarn run js-lint
-      - run: yarn run format-check
+      - run: <%- package_json.manager.native_run_command("js-lint") -%>
+      - run: <%- package_json.manager.native_run_command("format-check") -%>
   ruby_based_checks:
     runs-on: ubuntu-latest
     timeout-minutes: 20
@@ -105,7 +105,7 @@ jobs:
         with:
           node-version-file: ".node-version"
           cache: "yarn"
-      - run: yarn install --frozen-lockfile
+      - run: <%- package_json.manager.native_install_command(frozen: true) -%>
       - run: bundle exec rspec spec --format progress
       - name: Archive spec outputs
         uses: actions/upload-artifact@v3