make the transition non-instrusive

client/galaxy/scripts/layout/menu.js

@@ -162,11 +162,6 @@ var Collection = Backbone.Collection.extend({
             title: _l("Help"),
             tooltip: _l("Support, contact, and community"),
             menu: [
-                {
-                    title: _l("Galaxy Help"),
-                    url: options.helpsite_url,
-                    target: "_blank"
-                },
                 {
                     title: _l("Support"),
                     url: options.support_url,
@@ -224,6 +219,13 @@ var Collection = Backbone.Collection.extend({
                 target: "_blank"
             });
         }
+        if (options.helpsite_url) {
+            helpTab.menu.unshift({
+                    title: _l("Galaxy Help"),
+                    url: options.helpsite_url,
+                    target: "_blank"
+            });
+        }
         this.add(helpTab);
 
         //

config/galaxy.yml.sample

@@ -698,7 +698,7 @@ galaxy:
   #logo_url: /
 
   # The URL linked by the "Galaxy Help" link in the "Help" menu.
-  #helpsite_url: 'https://help.galaxyproject.org/'
+  #helpsite_url: ''
 
   # The URL linked by the "Wiki" link in the "Help" menu.
   #wiki_url: 'https://galaxyproject.org/'
@@ -1358,9 +1358,6 @@ galaxy:
   # of Galaxy's stable API.
   #enable_beta_workflow_modules: false
 
-  # Enable import and export of workflows as Galaxy Format 2 workflows.
-  #enable_beta_workflow_format: false
-
   # Following options only apply to workflows scheduled using the legacy
   # workflow run API (running workflows via a POST to /api/workflows).
   # Force usage of Galaxy's beta workflow scheduler under certain

doc/source/admin/galaxy_options.rst

@@ -1315,7 +1315,7 @@
 
 :Description:
     The URL linked by the "Galaxy Help" link in the "Help" menu.
-:Default: ``https://help.galaxyproject.org/``
+:Default: ````
 :Type: str
 
 
@@ -2820,17 +2820,6 @@
 :Type: bool
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``enable_beta_workflow_format``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Enable import and export of workflows as Galaxy Format 2
-    workflows.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``force_beta_workflow_scheduled_min_steps``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config.py

@@ -445,7 +445,7 @@ class Configuration(object):
         self.message_box_class = kwargs.get('message_box_class', 'info')
         self.support_url = kwargs.get('support_url', 'https://galaxyproject.org/support')
         self.citation_url = kwargs.get('citation_url', 'https://galaxyproject.org/citing-galaxy')
-        self.helpsite_url = kwargs.get('helpsite_url', 'https://help.galaxyproject.org/')
+        self.helpsite_url = kwargs.get('helpsite_url', None)
         self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
         self.blog_url = kwargs.get('blog_url', None)
         self.screencasts_url = kwargs.get('screencasts_url', None)

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -999,7 +999,7 @@ mapping:
 
       helpsite_url:
         type: str
-        default: https://help.galaxyproject.org/
+        default: ''
         required: false
         desc: |
           The URL linked by the "Galaxy Help" link in the "Help" menu.