Bootstrap.js bug was preventing loading the 'correct' way; resolved with an update.

config/plugins/visualizations/scatterplot/src/scatterplot.js

@@ -1,4 +1,7 @@
 import * as VisualizationModel from "mvc/visualization/visualization-model";
+import * as bootstrap from "bootstrap";
+import * as Backbone from "libs/backbone";
+import * as d3 from "libs/d3";
 
 /**
  *  Two Variable scatterplot visualization using d3

config/plugins/visualizations/scatterplot/templates/scatterplot.mako

@@ -28,15 +28,11 @@ ${h.stylesheet_link( root + 'plugins/visualizations/scatterplot/static/scatterpl
 window.Galaxy = { root: '${ root }' };
 </script>
 ${h.js( 'libs/jquery/jquery',
-        'libs/jquery/jquery-ui',
-        'libs/require',
-        'libs/bootstrap',
         'libs/underscore',
-        'libs/backbone',
         'libs/d3')}
-
 ${h.javascript_link( root + 'plugins/visualizations/scatterplot/static/scatterplot.bundle.js' )}
-    <script type="text/javascript">
+
+<script type="text/javascript">
     function getModel(){
         return new ScatterplotModel({
             id      : ${h.dumps( visualization_id )} || undefined,
@@ -48,7 +44,7 @@ ${h.javascript_link( root + 'plugins/visualizations/scatterplot/static/scatterpl
         return ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )};
     }
     window.jQuery = window.jquery = window.$;
-    </script>
+</script>
 
 </head>
 

config/plugins/visualizations/scatterplot/webpack.config.js

@@ -14,7 +14,7 @@ module.exports = {
         alias: {
             jquery: path.join(lroot, "jquery/jquery"),
             underscore: path.join(lroot, "underscore.js"),
-            backbone: path.join(lroot, "backbone.js")
+            backbone: path.join(lroot, "backbone.js"),
         }
     },
     module: {
@@ -28,9 +28,9 @@ module.exports = {
     },
     plugins: [
         new webpack.ProvidePlugin({
-            $: "jquery",
-            _: "underscore",
-            Backbone: "backbone"
+            jquery: "jquery",
+            jQuery: "jquery",
+            $: "jquery"
         })
     ]
 };