Update the issue tracker attribute on issue tracker change.

app/controllers/projects/services_controller.rb

@@ -17,6 +17,9 @@ class Projects::ServicesController < Projects::ApplicationController
 
   def update
     if @service.update_attributes(service_params)
+      if @service.activated? && @service.category == :issue_tracker
+        @project.update_attributes(issues_tracker: @service.to_param)
+      end
       redirect_to edit_project_service_path(@project, @service.to_param),
        notice: 'Successfully updated.'
     else

app/helpers/issues_helper.rb

@@ -16,7 +16,7 @@ module IssuesHelper
   def url_for_project_issues(project = @project)
     return '' if project.nil?
 
-    if project.using_issue_tracker?
+    if project.default_issues_tracker?
       project_issues_path(project)
     else
       project.external_issue_tracker.project_url
@@ -26,7 +26,7 @@ module IssuesHelper
   def url_for_new_issue(project = @project)
     return '' if project.nil?
 
-    if project.using_issue_tracker?
+    if project.default_issues_tracker?
       url = new_project_issue_path project_id: project
     else
       project.external_issue_tracker.new_issue_url
@@ -36,7 +36,7 @@ module IssuesHelper
   def url_for_issue(issue_iid, project = @project)
     return '' if project.nil?
 
-    if project.using_issue_tracker?
+    if project.default_issues_tracker?
       url = project_issue_url project_id: project, id: issue_iid
     else
       url = project.external_issue_tracker.issues_url

app/models/project.rb

@@ -308,11 +308,14 @@ class Project < ActiveRecord::Base
   end
 
   def default_issues_tracker?
-    self.issues_tracker == Project.issues_tracker.default_value
+    if external_issue_tracker
+      false
+    else
+      unless self.issues_tracker == Project.issues_tracker.default_value
+        self.update_attributes(issues_tracker: Project.issues_tracker.default_value)
+      end
+      true
     end
-
-  def external_issues_tracker_enabled?
-    external_issues_trackers.any?
   end
 
   def external_issues_trackers
@@ -323,10 +326,6 @@ class Project < ActiveRecord::Base
     @external_issues_tracker ||= external_issues_trackers.select(&:activated?).first
   end
 
-  def using_issue_tracker?
-    default_issues_tracker? || !external_issues_tracker_enabled?
-  end
-
   def can_have_issues_tracker_id?
     self.issues_enabled && !self.default_issues_tracker?
   end

lib/gitlab/markdown.rb

@@ -208,7 +208,7 @@ module Gitlab
     end
 
     def reference_issue(identifier, project = @project, prefix_text = nil)
-      if project.using_issue_tracker?
+      if project.default_issues_tracker?
         if project.issue_exists? identifier
           url = url_for_issue(identifier, project)
           title = title_for_issue(identifier, project)