diff --git a/static/scripts/autocomplete_tagging.js b/static/scripts/galaxy.autocom_tagging.js
similarity index 100%
rename from static/scripts/autocomplete_tagging.js
rename to static/scripts/galaxy.autocom_tagging.js
diff --git a/static/scripts/ui.core.js b/static/scripts/libs/jquery/jquery.ui.core.js
similarity index 100%
rename from static/scripts/ui.core.js
rename to static/scripts/libs/jquery/jquery.ui.core.js
diff --git a/static/scripts/packed/autocomplete_tagging.js b/static/scripts/packed/galaxy.autocom_tagging.js
similarity index 100%
rename from static/scripts/packed/autocomplete_tagging.js
rename to static/scripts/packed/galaxy.autocom_tagging.js
diff --git a/static/scripts/packed/ui.core.js b/static/scripts/packed/libs/jquery/jquery.ui.core.js
similarity index 100%
rename from static/scripts/packed/ui.core.js
rename to static/scripts/packed/libs/jquery/jquery.ui.core.js
diff --git a/templates/admin/data_admin/data_form.mako b/templates/admin/data_admin/data_form.mako
index dde487ff86d..000652ebd63 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_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 fd46c54c927..c0debdb4fd1 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_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 256d9e47377..cba4f802deb 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_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 011636ed718..44a43f9399f 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>
 
-${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+${h.js( "libs/jquery/jquery.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 765670d0b19..f5420813256 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", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.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 b24d031e6ca..7a80d7e976d 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", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index aae0f1682de..bf56e9bee31 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", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="datatype( dataset, datatypes )">
diff --git a/templates/display_base.mako b/templates/display_base.mako
index bd9305d1dd0..a556138b756 100644
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -33,7 +33,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/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", 
+            "galaxy.autocom_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", "libs/farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 74c523db946..8c4f522d6f4 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -52,7 +52,7 @@
 </%def>
 
 <%def name="grid_javascripts()">
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging", "libs/jquery/jquery.rating" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_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/library/common/ldda_edit_info.mako b/templates/library/common/ldda_edit_info.mako
index 38311e5ea04..e28156bcecc 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/move_library_item.mako b/templates/library/common/move_library_item.mako
index 2f6c7483eec..43284dd2e60 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/upload.mako b/templates/library/common/upload.mako
index 769d2e1d74d..1f1b33bf981 100644
--- a/templates/library/common/upload.mako
+++ b/templates/library/common/upload.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/page/editor.mako b/templates/page/editor.mako
index f82c9d920e5..0a4c53f11da 100644
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -22,7 +22,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "libs/json2", "libs/jquery/jstorage",
-            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")}    
+            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "galaxy.autocom_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 550500857f8..e841a6f5630 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/requests/common/find_samples.mako b/templates/requests/common/find_samples.mako
index 83f52ba0d22..0617428fc49 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("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 6d4cf9f7b64..83ef56d4184 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( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 
 <script type="text/javascript">
 
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index 958b11adbd7..0aa28c2199e 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -17,7 +17,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.templates( "tool_link", "panel_section", "tool_search" )}
-    ${h.js( "galaxy.base", "libs/json2", "autocomplete_tagging", "mvc/tools", "libs/bootstrap" )}
+    ${h.js( "galaxy.base", "libs/json2", "galaxy.autocom_tagging", "mvc/tools", "libs/bootstrap" )}
     
     <%
         # Set up for creating tool panel.
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 931eb9f97e5..25804b16cad 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( "libs/jquery/jquery.rating", "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 45602e5e939..3cf779c465a 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -28,7 +28,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
     <script type="text/javascript">
     $( function() {
diff --git a/templates/workflow/edit_attributes.mako b/templates/workflow/edit_attributes.mako
index 09f396a97cb..b707f4abe68 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", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 %if msg:
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index 1d8e7b75f45..d3735a9c46c 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -36,7 +36,7 @@
             "galaxy.base",
             "galaxy.workflow_editor.canvas",
             "libs/jquery/jquery.autocomplete",
-            "autocomplete_tagging")}
+            "galaxy.autocom_tagging")}
 
     <!--[if lt IE 7]>
     <script type='text/javascript'>