diff --git a/static/scripts/jquery.event.drag.js.patch b/static/scripts/jquery.event.drag.js.patch
deleted file mode 100644
index 1c5178021e0..00000000000
--- a/static/scripts/jquery.event.drag.js.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-96c96
-< 			if ( drag.dragging ){
----
-> 			if ( drag.dragging ) {
-99c99,101
-< 				}
----
-> 			} else {
-> 				hijack( event, "dragclickonly", elem );
-> 			}
diff --git a/static/scripts/jqtouch.js b/static/scripts/libs/jquery/jqtouch.js
similarity index 100%
rename from static/scripts/jqtouch.js
rename to static/scripts/libs/jquery/jqtouch.js
diff --git a/static/scripts/jquery.autocomplete.js b/static/scripts/libs/jquery/jquery.autocomplete.js
similarity index 100%
rename from static/scripts/jquery.autocomplete.js
rename to static/scripts/libs/jquery/jquery.autocomplete.js
diff --git a/static/scripts/jquery.cookie.js b/static/scripts/libs/jquery/jquery.cookie.js
similarity index 100%
rename from static/scripts/jquery.cookie.js
rename to static/scripts/libs/jquery/jquery.cookie.js
diff --git a/static/scripts/jquery.dynatree.js b/static/scripts/libs/jquery/jquery.dynatree.js
similarity index 100%
rename from static/scripts/jquery.dynatree.js
rename to static/scripts/libs/jquery/jquery.dynatree.js
diff --git a/static/scripts/jquery.event.drag.js b/static/scripts/libs/jquery/jquery.event.drag.js
similarity index 100%
rename from static/scripts/jquery.event.drag.js
rename to static/scripts/libs/jquery/jquery.event.drag.js
diff --git a/static/scripts/jquery.event.drop.js b/static/scripts/libs/jquery/jquery.event.drop.js
similarity index 100%
rename from static/scripts/jquery.event.drop.js
rename to static/scripts/libs/jquery/jquery.event.drop.js
diff --git a/static/scripts/jquery.event.hover.js b/static/scripts/libs/jquery/jquery.event.hover.js
similarity index 100%
rename from static/scripts/jquery.event.hover.js
rename to static/scripts/libs/jquery/jquery.event.hover.js
diff --git a/static/scripts/jquery.form.js b/static/scripts/libs/jquery/jquery.form.js
similarity index 100%
rename from static/scripts/jquery.form.js
rename to static/scripts/libs/jquery/jquery.form.js
diff --git a/static/scripts/jquery.js b/static/scripts/libs/jquery/jquery.js
similarity index 100%
rename from static/scripts/jquery.js
rename to static/scripts/libs/jquery/jquery.js
diff --git a/static/scripts/jquery.mousewheel.js b/static/scripts/libs/jquery/jquery.mousewheel.js
similarity index 100%
rename from static/scripts/jquery.mousewheel.js
rename to static/scripts/libs/jquery/jquery.mousewheel.js
diff --git a/static/scripts/jquery.rating.js b/static/scripts/libs/jquery/jquery.rating.js
similarity index 100%
rename from static/scripts/jquery.rating.js
rename to static/scripts/libs/jquery/jquery.rating.js
diff --git a/static/scripts/jquery.tipsy.js b/static/scripts/libs/jquery/jquery.tipsy.js
similarity index 100%
rename from static/scripts/jquery.tipsy.js
rename to static/scripts/libs/jquery/jquery.tipsy.js
diff --git a/static/scripts/jquery.ui.sortable.slider.js b/static/scripts/libs/jquery/jquery.ui.sortable.slider.js
similarity index 100%
rename from static/scripts/jquery.ui.sortable.slider.js
rename to static/scripts/libs/jquery/jquery.ui.sortable.slider.js
diff --git a/static/scripts/jquery.wymeditor.js b/static/scripts/libs/jquery/jquery.wymeditor.js
similarity index 100%
rename from static/scripts/jquery.wymeditor.js
rename to static/scripts/libs/jquery/jquery.wymeditor.js
diff --git a/static/scripts/jstorage.js b/static/scripts/libs/jquery/jstorage.js
similarity index 100%
rename from static/scripts/jstorage.js
rename to static/scripts/libs/jquery/jstorage.js
diff --git a/static/scripts/packed/jqtouch.js b/static/scripts/packed/libs/jquery/jqtouch.js
similarity index 100%
rename from static/scripts/packed/jqtouch.js
rename to static/scripts/packed/libs/jquery/jqtouch.js
diff --git a/static/scripts/packed/jquery.autocomplete.js b/static/scripts/packed/libs/jquery/jquery.autocomplete.js
similarity index 100%
rename from static/scripts/packed/jquery.autocomplete.js
rename to static/scripts/packed/libs/jquery/jquery.autocomplete.js
diff --git a/static/scripts/packed/jquery.cookie.js b/static/scripts/packed/libs/jquery/jquery.cookie.js
similarity index 100%
rename from static/scripts/packed/jquery.cookie.js
rename to static/scripts/packed/libs/jquery/jquery.cookie.js
diff --git a/static/scripts/packed/jquery.dynatree.js b/static/scripts/packed/libs/jquery/jquery.dynatree.js
similarity index 100%
rename from static/scripts/packed/jquery.dynatree.js
rename to static/scripts/packed/libs/jquery/jquery.dynatree.js
diff --git a/static/scripts/packed/jquery.event.drag.js b/static/scripts/packed/libs/jquery/jquery.event.drag.js
similarity index 100%
rename from static/scripts/packed/jquery.event.drag.js
rename to static/scripts/packed/libs/jquery/jquery.event.drag.js
diff --git a/static/scripts/packed/jquery.event.drop.js b/static/scripts/packed/libs/jquery/jquery.event.drop.js
similarity index 100%
rename from static/scripts/packed/jquery.event.drop.js
rename to static/scripts/packed/libs/jquery/jquery.event.drop.js
diff --git a/static/scripts/packed/jquery.event.hover.js b/static/scripts/packed/libs/jquery/jquery.event.hover.js
similarity index 100%
rename from static/scripts/packed/jquery.event.hover.js
rename to static/scripts/packed/libs/jquery/jquery.event.hover.js
diff --git a/static/scripts/packed/jquery.form.js b/static/scripts/packed/libs/jquery/jquery.form.js
similarity index 100%
rename from static/scripts/packed/jquery.form.js
rename to static/scripts/packed/libs/jquery/jquery.form.js
diff --git a/static/scripts/packed/jquery.js b/static/scripts/packed/libs/jquery/jquery.js
similarity index 100%
rename from static/scripts/packed/jquery.js
rename to static/scripts/packed/libs/jquery/jquery.js
diff --git a/static/scripts/packed/jquery.mousewheel.js b/static/scripts/packed/libs/jquery/jquery.mousewheel.js
similarity index 100%
rename from static/scripts/packed/jquery.mousewheel.js
rename to static/scripts/packed/libs/jquery/jquery.mousewheel.js
diff --git a/static/scripts/packed/jquery.rating.js b/static/scripts/packed/libs/jquery/jquery.rating.js
similarity index 100%
rename from static/scripts/packed/jquery.rating.js
rename to static/scripts/packed/libs/jquery/jquery.rating.js
diff --git a/static/scripts/packed/jquery.tipsy.js b/static/scripts/packed/libs/jquery/jquery.tipsy.js
similarity index 100%
rename from static/scripts/packed/jquery.tipsy.js
rename to static/scripts/packed/libs/jquery/jquery.tipsy.js
diff --git a/static/scripts/packed/jquery.ui.sortable.slider.js b/static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js
similarity index 100%
rename from static/scripts/packed/jquery.ui.sortable.slider.js
rename to static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js
diff --git a/static/scripts/packed/jquery.wymeditor.js b/static/scripts/packed/libs/jquery/jquery.wymeditor.js
similarity index 100%
rename from static/scripts/packed/jquery.wymeditor.js
rename to static/scripts/packed/libs/jquery/jquery.wymeditor.js
diff --git a/static/scripts/packed/jstorage.js b/static/scripts/packed/libs/jquery/jstorage.js
similarity index 100%
rename from static/scripts/packed/jstorage.js
rename to static/scripts/packed/libs/jquery/jstorage.js
diff --git a/templates/admin/data_admin/data_form.mako b/templates/admin/data_admin/data_form.mako
index 1ed3e25f3c3..dde487ff86d 100644
--- a/templates/admin/data_admin/data_form.mako
+++ b/templates/admin/data_admin/data_form.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/generic_error.mako b/templates/admin/data_admin/generic_error.mako
index 2c70ed051df..fd46c54c927 100644
--- a/templates/admin/data_admin/generic_error.mako
+++ b/templates/admin/data_admin/generic_error.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/local_data.mako b/templates/admin/data_admin/local_data.mako
index 84f0f9e650c..256d9e47377 100644
--- a/templates/admin/data_admin/local_data.mako
+++ b/templates/admin/data_admin/local_data.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/requests/select_datasets_to_transfer.mako b/templates/admin/requests/select_datasets_to_transfer.mako
index 991d9f76c1b..011636ed718 100644
--- a/templates/admin/requests/select_datasets_to_transfer.mako
+++ b/templates/admin/requests/select_datasets_to_transfer.mako
@@ -8,7 +8,7 @@
    ${common_javascripts()}
 </%def>
 
-${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
+${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
 ${h.css( "dynatree_skin/ui.dynatree" )}
 
 <script type="text/javascript">
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
index 1b9065a5077..765670d0b19 100644
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
 </%def>
 
diff --git a/templates/admin/tool_shed_repository/browse_tool_dependency.mako b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
index 5e50832704b..b24d031e6ca 100644
--- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako
+++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 
diff --git a/templates/base.mako b/templates/base.mako
index 1b860d8ab2c..c54db53162c 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -26,7 +26,7 @@
   ## <!--[if lt IE 7]>
   ## <script type='text/javascript' src="/static/scripts/IE7.js"> </script>
   ## <![endif]-->
-  ${h.js( "jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
+  ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
   <script type="text/javascript">
       // Set up needed paths.
       var galaxy_paths = new GalaxyPaths({
diff --git a/templates/base_panels.mako b/templates/base_panels.mako
index 092a5650736..9d9e5503758 100644
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -48,7 +48,7 @@
     <!--[if lt IE 7]>
     ${h.js( 'IE7', 'ie7-recalc' )}
     <![endif]-->
-    ${h.js( 'jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
+    ${h.js( 'libs/jquery/jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
     <script type="text/javascript">
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({
@@ -73,7 +73,7 @@
 <%def name="late_javascripts()">
     ## Scripts can be loaded later since they progressively add features to
     ## the panels, but do not change layout
-    ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'jquery.rating', 'galaxy.base', 'galaxy.panels' )}
+    ${h.js( 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.form', 'libs/jquery/jquery.rating', 'galaxy.base', 'galaxy.panels' )}
     <script type="text/javascript">
         
     ensure_dd_helper();
diff --git a/templates/dataset/copy_view.mako b/templates/dataset/copy_view.mako
index 7b781f52a95..d908a163b5b 100644
--- a/templates/dataset/copy_view.mako
+++ b/templates/dataset/copy_view.mako
@@ -4,7 +4,7 @@
 <%def name="javascripts()">
 
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
     
     <script type="text/javascript">
         $(function() {
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 33bd3363a6e..aae0f1682de 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -11,7 +11,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${message_ns.javascripts()}
-    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="datatype( dataset, datatypes )">
diff --git a/templates/display_base.mako b/templates/display_base.mako
index 019ada2ad48..f21d9ba0298 100644
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -32,9 +32,9 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "bootstrap", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "jquery.rating", 
-            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "jquery.event.drag", "jquery.mousewheel", 
-            "jquery.autocomplete", "jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
+    ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
+            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
+            "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
         
diff --git a/templates/form.mako b/templates/form.mako
index 7cc2d6e3c2e..a27939be1c3 100644
--- a/templates/form.mako
+++ b/templates/form.mako
@@ -26,7 +26,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete")}
+    ${h.js("libs/jquery/jquery.autocomplete")}
     <script type="text/javascript">
         $(function(){
             $("input:text:first").focus();
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 8c6c4bdcae1..74c523db946 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -52,7 +52,7 @@
 </%def>
 
 <%def name="grid_javascripts()">
-    ${h.js("jquery.autocomplete", "autocomplete_tagging", "jquery.rating" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging", "libs/jquery/jquery.rating" )}
     <script type="text/javascript">
         // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are
         // not appended to the identifier of a nested array.
diff --git a/templates/history/view.mako b/templates/history/view.mako
index fdef5575a9f..56e17d8386d 100644
--- a/templates/history/view.mako
+++ b/templates/history/view.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "jquery", "json2", "jstorage" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery", "json2", "libs/jquery/jstorage" )}
     <script type="text/javascript">
         $(function() {
             init_history_items( $("div.historyItemWrapper"), false, "nochanges" );
diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index ca9fc53d1fc..ffa3445f696 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -49,7 +49,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js("json2")}
-    ${h.js("jstorage")}
+    ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
     ${self.grid_javascripts()}
 </%def>
diff --git a/templates/library/common/import_datasets_to_histories.mako b/templates/library/common/import_datasets_to_histories.mako
index d3a5bb15d44..8b823a2f098 100644
--- a/templates/library/common/import_datasets_to_histories.mako
+++ b/templates/library/common/import_datasets_to_histories.mako
@@ -5,7 +5,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
     <script type="text/javascript">
         $(function() {
             $("#select-multiple").click(function() {
diff --git a/templates/library/common/ldda_edit_info.mako b/templates/library/common/ldda_edit_info.mako
index c32326af961..38311e5ea04 100644
--- a/templates/library/common/ldda_edit_info.mako
+++ b/templates/library/common/ldda_edit_info.mako
@@ -5,7 +5,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/library_dataset_search_results.mako b/templates/library/common/library_dataset_search_results.mako
index 3a8c41ffca1..85dc41bfb4b 100644
--- a/templates/library/common/library_dataset_search_results.mako
+++ b/templates/library/common/library_dataset_search_results.mako
@@ -46,7 +46,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jstorage")}
+    ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
 </%def>
 
diff --git a/templates/library/common/move_library_item.mako b/templates/library/common/move_library_item.mako
index 5a53b734fe2..2f6c7483eec 100644
--- a/templates/library/common/move_library_item.mako
+++ b/templates/library/common/move_library_item.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/upload.mako b/templates/library/common/upload.mako
index b8dffce267e..769d2e1d74d 100644
--- a/templates/library/common/upload.mako
+++ b/templates/library/common/upload.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/mobile/index.mako b/templates/mobile/index.mako
index 16e0c5f1fdf..2879520dc67 100644
--- a/templates/mobile/index.mako
+++ b/templates/mobile/index.mako
@@ -26,8 +26,8 @@
     </style>
     
     <style type="text/css" media="screen">@import "${h.url_for('/static/jqtouch/jqtouch.css')}";</style>
-    <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script>
-    <script type="text/javascript" src="${h.url_for('/static/scripts/jqtouch.js')}"></script>
+    <script type="text/javascript" src="${h.url_for('/static/scripts/libs/jquery/jquery.js')}"></script>
+    <script type="text/javascript" src="${h.url_for('/static/scripts/libs/jquery/jqtouch.js')}"></script>
     <script type="text/javascript" charset="utf-8">
         $(document).jQTouch( {
             icon: "${h.url_for('static/images/galaxyIcon_noText.png')}",
diff --git a/templates/page/editor.mako b/templates/page/editor.mako
index 7a9c7e4a648..ae68886515e 100644
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -21,8 +21,8 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage",
-            "galaxy.base", "jquery.wymeditor", "jquery.autocomplete", "autocomplete_tagging")}    
+    ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "json2", "libs/jquery/jstorage",
+            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")}    
     <script type="text/javascript">
             
     // Useful Galaxy stuff.
diff --git a/templates/requests/common/create_request.mako b/templates/requests/common/create_request.mako
index ac0b5e70b73..550500857f8 100644
--- a/templates/requests/common/create_request.mako
+++ b/templates/requests/common/create_request.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/requests/common/find_samples.mako b/templates/requests/common/find_samples.mako
index 29512adef24..83f52ba0d22 100644
--- a/templates/requests/common/find_samples.mako
+++ b/templates/requests/common/find_samples.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 5dcfdc768d7..4eb4b8dff63 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -17,7 +17,7 @@
 <meta http-equiv="Pragma" content="no-cache">
 
 ${h.css( "base", "history", "autocomplete_tagging" )}
-${h.js( "jquery", "bootstrap", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 
 <script type="text/javascript">
 
diff --git a/templates/tool_form.mako b/templates/tool_form.mako
index 25068f511d5..84562cbc719 100644
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -12,7 +12,7 @@
 </%def>
 
 <%def name="javascripts()">
-    ${h.js( "jquery", "galaxy.panels", "galaxy.base", "jquery.autocomplete", "jstorage" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )}
     <script type="text/javascript">
     $(function() {
         $(window).bind("refresh_on_change", function() {
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index dffc5eaa8f9..59a5e3e3b16 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -21,7 +21,7 @@ ${parent.javascripts()}
   <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "bootstrap", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider", "farbtastic" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "libs/jquery/jquery", "bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "farbtastic" )}
 
 <script type="text/javascript">
     //
diff --git a/templates/visualization/sweepster.mako b/templates/visualization/sweepster.mako
index e9d0ba176f6..65ee81ddce0 100644
--- a/templates/visualization/sweepster.mako
+++ b/templates/visualization/sweepster.mako
@@ -108,7 +108,7 @@
 
     ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )}
     ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/sweepster", 
-            "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider" )}
+            "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider" )}
 
     <script type="text/javascript">
         var viz;
diff --git a/templates/webapps/community/admin/index.mako b/templates/webapps/community/admin/index.mako
index 50085558edc..66b7949b3ee 100644
--- a/templates/webapps/community/admin/index.mako
+++ b/templates/webapps/community/admin/index.mako
@@ -18,7 +18,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index 16c40dc44c6..6e8c293e660 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -19,7 +19,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 1d3c5ab2761..931eb9f97e5 100644
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -57,7 +57,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating", "ui.core", "jquery.cookie", "jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.rating", "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index 4156af5710a..e8128247ca5 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -63,7 +63,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 494077e599e..84cc5c778ed 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -58,7 +58,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/rate_repository.mako b/templates/webapps/community/repository/rate_repository.mako
index 37b13346e32..189fbb13a84 100644
--- a/templates/webapps/community/repository/rate_repository.mako
+++ b/templates/webapps/community/repository/rate_repository.mako
@@ -61,7 +61,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 %if message:
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 2b71e897ab7..45602e5e939 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -23,12 +23,12 @@
 
 <%def name="stylesheets()">
     ${parent.stylesheets()}
-    ${h.css( "jquery.rating", "dynatree_skin/ui.dynatree" )}
+    ${h.css( "libs/jquery/jquery.rating", "dynatree_skin/ui.dynatree" )}
 </%def>
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
     <script type="text/javascript">
     $( function() {
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index 6a6d8bcbf5b..1f02b737c4d 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -36,7 +36,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 <br/><br/>
diff --git a/templates/webapps/community/repository/view_changeset.mako b/templates/webapps/community/repository/view_changeset.mako
index 00a65ec1dd0..16fa2bda032 100644
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -37,7 +37,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 <br/><br/>
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index f53d46bf4a1..12c2e531ec4 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -59,7 +59,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index a4dd17ff776..778825be64b 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -22,7 +22,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako
index 29273bb10bf..ce571f7b18a 100644
--- a/templates/webapps/reports/index.mako
+++ b/templates/webapps/reports/index.mako
@@ -26,7 +26,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="left_panel()">
diff --git a/templates/workflow/edit_attributes.mako b/templates/workflow/edit_attributes.mako
index 5a63cad4eb1..09f396a97cb 100644
--- a/templates/workflow/edit_attributes.mako
+++ b/templates/workflow/edit_attributes.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 %if msg:
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index b589cba239b..b6ef46d6425 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -25,17 +25,17 @@
       <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
     <![endif]-->
 
-    ${h.js( "jquery",
+    ${h.js( "libs/jquery/jquery",
             "bootstrap",
-            "jquery.event.drag",
-            "jquery.event.drop",
-            "jquery.event.hover",
-            "jquery.form",
+            "libs/jquery/jquery.event.drag",
+            "libs/jquery/jquery.event.drop",
+            "libs/jquery/jquery.event.hover",
+            "libs/jquery/jquery.form",
             "json2",
-            "jstorage",
+            "libs/jquery/jstorage",
             "galaxy.base",
             "galaxy.workflow_editor.canvas",
-            "jquery.autocomplete",
+            "libs/jquery/jquery.autocomplete",
             "autocomplete_tagging")}
 
     <!--[if lt IE 7]>
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index 3c85da423c2..b12790f05f1 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -2,7 +2,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.autocomplete", "bootstrap" )}
+    ${h.js( "libs/jquery/jquery.autocomplete", "bootstrap" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){