diff --git a/.rubocop.yml b/.rubocop.yml
new file mode 100644
index 0000000..43d23b3
--- /dev/null
+++ b/.rubocop.yml
@@ -0,0 +1,3 @@
+inherit_gem:
+  rubocop-dmp_roadmap:
+    - config/default.yml
diff --git a/Gemfile b/Gemfile
index 74904ab..109bd9c 100644
--- a/Gemfile
+++ b/Gemfile
@@ -181,15 +181,12 @@
   gem 'chromedriver-helper', ">= 1.2.0"
 end
 
-group :ci do
+group :ci, :development do
   # Security vulnerability scanner for Ruby on Rails. (http://brakemanscanner.org)
   gem "brakeman"
 
   # Automatic Ruby code style checking tool. (https://github.com/rubocop-hq/rubocop)
-  gem "rubocop"
-
-  # Code style checking for RSpec files (https://github.com/rubocop-hq/rubocop-rspec)
-  gem "rubocop-rspec"
+  gem "rubocop-dmp_roadmap"
 
   # Helper gem to require bundler-audit (http://github.com/stewartmckee/bundle-audit)
   gem "bundle-audit"
@@ -216,4 +213,8 @@
 
   # help to kill N+1 queries and unused eager loading. (https://github.com/flyerhzm/bullet)
   gem "bullet"
+
+  gem "yard"
+
+  gem "yard-tomdoc"
 end
diff --git a/Gemfile.lock b/Gemfile.lock
index 0a1f14d..827f65f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -315,6 +315,13 @@
       rainbow (>= 2.2.2, < 4.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (~> 1.0, >= 1.0.1)
+    rubocop-dmp_roadmap (1.0.0)
+      rubocop (>= 0.58.2)
+      rubocop-rails_config (>= 0.2.2)
+      rubocop-rspec (>= 1.27.0)
+    rubocop-rails_config (0.2.2)
+      railties (>= 3.0)
+      rubocop (~> 0.56)
     rubocop-rspec (1.27.0)
       rubocop (>= 0.56.0)
     ruby-progressbar (1.9.0)
@@ -356,6 +363,7 @@
       rack (>= 1, < 3)
     thor (0.20.0)
     thread_safe (0.3.6)
+    tomparse (0.4.2)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
     unicode-display_width (1.4.0)
@@ -374,6 +382,10 @@
     wkhtmltopdf-binary (0.12.3.1)
     xpath (3.1.0)
       nokogiri (~> 1.8)
+    yard (0.9.14)
+    yard-tomdoc (0.7.1)
+      tomparse (>= 0.4.0)
+      yard
 
 PLATFORMS
   ruby
@@ -423,7 +435,7 @@
   responders (~> 2.0)
   rspec-collection_matchers
   rspec-rails
-  rubocop
+  rubocop-dmp_roadmap
   rubocop-rspec
   ruby_dig
   selenium-webdriver (>= 3.13.1)
@@ -436,6 +448,8 @@
   webmock
   wicked_pdf
   wkhtmltopdf-binary
+  yard
+  yard-tomdoc
 
 RUBY VERSION
    ruby 2.4.4p296
diff --git a/app/controllers/api/v0/base_controller.rb b/app/controllers/api/v0/base_controller.rb
index c8edddd..a3c3490 100644
--- a/app/controllers/api/v0/base_controller.rb
+++ b/app/controllers/api/v0/base_controller.rb
@@ -49,34 +49,39 @@
       end
 
       private
-      # returns the resource from the created instance variable
-      # @return [Object]
+
+      # The resource from the created instance variable
+      #
+      # Returns Object
       def get_resource
         instance_variable_get("@#{resource_name}")
       end
 
-      # Returns the allowed parameters for searching
-      # Override this method in each API controller
-      # to permit additional parameters to search on
-      # @return [Hash]
+      # The allowed parameters for searching. Override this method in each API
+      # controller to permit additional parameters to search on
+      #
+      # Returns Hash
       def query_params
         {}
       end
 
-      # Returns the allowed parameters for pagination
-      # @return [Hash]
+      # The allowed parameters for pagination
+      #
+      # Returns Hash
       def page_params
         params.permit(:page, :page_size)
       end
 
       # The resource class based on the controller
-      # @return [Class]
+      #
+      # Returns Object
       def resource_class
         @resource_class ||= resource_name.classify.constantize
       end
 
       # The singular name for the resource class based on the controller
-      # @return [String]
+      #
+      # Returns String
       def resource_name
         @resource_name ||= self.controller_name.singularize
       end
diff --git a/app/controllers/api/v0/statistics_controller.rb b/app/controllers/api/v0/statistics_controller.rb
index 8d84bd4..1223121 100644
--- a/app/controllers/api/v0/statistics_controller.rb
+++ b/app/controllers/api/v0/statistics_controller.rb
@@ -4,11 +4,12 @@
       before_action :authenticate
 
       # GET /api/v0/statistics/users_joined?start_date=&end_date=&org_id=
+      #
       # Returns the number of users joined for the user's org.
       # If start_date is passed, only counts those with created_at is >= than start_date
       # If end_date is passed, only counts those with created_at is <= than end_date are
-      # If org_id is passed and user has super_admin privileges that counter is performed against org_id param instead of user's org
-      # @return
+      # If org_id is passed and user has super_admin privileges that counter is performed
+      # against org_id param instead of user's org
       def users_joined
         raise Pundit::NotAuthorizedError unless Api::V0::StatisticsPolicy.new(@user, :statistics).users_joined?
 
@@ -124,9 +125,9 @@
       end
 
       ##
-      # GET
-      # @return the number of DMPs using the specified template between the optional specified dates
-      # ensures that the template is owned/created by the caller's organisation
+      # Displays the number of DMPs using the specified template between the optional
+      # specified dates ensures that the template is owned/created by the caller's
+      # organisation
       def using_template
         org_templates = @user.org.templates.where(customization_of: nil)
         raise Pundit::NotAuthorizedError unless Api::V0::StatisticsPolicy.new(@user, org_templates.first).using_template?
@@ -152,9 +153,9 @@
 
       ##
       # GET
-      # @return a list of templates with their titles, ids, and uses between the optional specified dates
-      # the uses are restricted to DMPs created by users of the same organisation
-      # as the user who ititiated the call
+      # Renders a list of templates with their titles, ids, and uses between the optional
+      # specified dates the uses are restricted to DMPs created by users of the same
+      # organisation as the user who ititiated the call.
       def plans_by_template
         raise Pundit::NotAuthorizedError unless Api::V0::StatisticsPolicy.new(@user, :statistics).plans_by_template?
         org_projects = []
@@ -181,11 +182,11 @@
         respond_with @templates
       end
 
-      ##
       # GET
-      # @return a list of DMPs metadata, provided the DMPs were created between the optional specified dates
-      # DMPs must be owned by a user who's organisation is the same as the user
-      # who generates the call
+      #
+      # Renders a list of DMPs metadata, provided the DMPs were created between the
+      # optional specified dates DMPs must be owned by a user who's organisation is the
+      # same as the user who generates the call.
       def plans
         raise Pundit::NotAuthorizedError unless Api::V0::StatisticsPolicy.new(@user, :statistics).plans?
         @org_plans = []
@@ -202,32 +203,34 @@
 
 
       private
-        ##
-        # takes in an array of active_reccords and restricts the range of dates
-        # to those specified in the params
-        #
-        # @param objects [Array<ActiveReccord>] any active_reccord reccords which
-        #   have the "created_at" field specified
-        # @return [Array<ActiveReccord>] filtered list of objects
-        def restrict_date_range( objects )
-          # set start_date to either passed param, or beginning of time
-          start_date = params[:start_date].blank? ? Date.new(0) : Date.strptime(params[:start_date], "%Y-%m-%d")
-          # set end_date to either passed param or now
-          end_date = params[:end_date].blank? ? Date.today : Date.strptime(params[:end_date], "%Y-%m-%d")
 
-          filtered = []
-          objects.each do |obj|
-            # apperantly things can have nil created_at
-            if obj.created_at.blank?
-              if params[:start_date].blank? && params[:end_date].blank?
-                filtered += [obj]
-              end
-            elsif start_date <= obj.created_at.to_date && end_date >= obj.created_at.to_date
+      ##
+      # Takes in an array of active_reccords and restricts the range of dates
+      # to those specified in the params
+      #
+      # objects - any active_reccord reccords which have the "created_at" field specified
+      #
+      # Returns Array
+      def restrict_date_range( objects )
+        # set start_date to either passed param, or beginning of time
+        start_date = params[:start_date].blank? ? Date.new(0) : Date.strptime(params[:start_date], "%Y-%m-%d")
+        # set end_date to either passed param or now
+        end_date = params[:end_date].blank? ? Date.today : Date.strptime(params[:end_date], "%Y-%m-%d")
+
+        filtered = []
+        objects.each do |obj|
+          # apperantly things can have nil created_at
+          if obj.created_at.blank?
+            if params[:start_date].blank? && params[:end_date].blank?
               filtered += [obj]
             end
+          elsif start_date <= obj.created_at.to_date && end_date >= obj.created_at.to_date
+            filtered += [obj]
           end
-          return filtered
         end
+        return filtered
+      end
+
     end
   end
 end
diff --git a/app/controllers/api/v0/templates_controller.rb b/app/controllers/api/v0/templates_controller.rb
index 03999f8..b1dea9f 100644
--- a/app/controllers/api/v0/templates_controller.rb
+++ b/app/controllers/api/v0/templates_controller.rb
@@ -4,9 +4,9 @@
       before_action :authenticate
 
 
-      ##
       # GET
-      # @return a list of templates ordered by organisation
+      #
+      # Renders a list of templates ordered by organisation
       def index
         # check if the user has permissions to use the templates API
         raise Pundit::NotAuthorizedError unless Api::V0::TemplatePolicy.new(@user, :guidance_group).index?
diff --git a/app/controllers/concerns/conditional_user_mailer.rb b/app/controllers/concerns/conditional_user_mailer.rb
index d8bc509..560b93f 100644
--- a/app/controllers/concerns/conditional_user_mailer.rb
+++ b/app/controllers/concerns/conditional_user_mailer.rb
@@ -5,13 +5,11 @@
   # Executes a given block passed if the recipient user has the preference
   # email key enabled
   #
-  # @param recipients {User | Enumerable } User object or any object that
-  # includes Enumerable class
+  # recipients - User or Enumerable object or any object that includes Enumerable class
+  # key        - A key (dot notation) whose value is true/false and belongs to
+  #              prefences.email (see config/branding.yml)
   #
-  # @param key {String} - A key (dot notation) whose value is true/false and
-  # belongs to prefences.email (see config/branding.yml)
-  #
-  # Returns true or false
+  # Returns Boolean
   def deliver_if(recipients: [], key:, &block)
     return false unless block_given?
 
diff --git a/app/controllers/concerns/versionable.rb b/app/controllers/concerns/versionable.rb
index aa633d7..c1893e9 100644
--- a/app/controllers/concerns/versionable.rb
+++ b/app/controllers/concerns/versionable.rb
@@ -1,11 +1,12 @@
 module Versionable
 
-  ##
   # Takes in a Template, phase, Section, Question, or Annotaion
   # IF the template is published, generates a new template
   # finds the passed object in the new template
-  # @param obj - Template, Phase, Section, Question, Annotation
-  # @return type_of(obj)
+  #
+  # obj - Template, Phase, Section, Question, Annotation
+  #
+  # Returns ActiveRecord::Base
   def get_modifiable(obj)
     if obj.respond_to?(:template)
       template = obj.template
diff --git a/app/controllers/passwords_controller.rb b/app/controllers/passwords_controller.rb
index 9116fb1..fc23f4b 100644
--- a/app/controllers/passwords_controller.rb
+++ b/app/controllers/passwords_controller.rb
@@ -1,17 +1,18 @@
 class PasswordsController < Devise::PasswordsController
-	
+
 	protected
-	
+
 	def after_resetting_password_path_for(resource)
     root_path
   end
-  
+
   ##
   # Override Devise default behaviour by sending user to the home page
   # after the password reset email has been sent
   #
-  # @resource_name [String] The user's email address
-  # ---------------------------------------------------------------------
+  # resource_name - The user's email address
+  #
+  # Returns String
   def after_sending_reset_password_instructions_path_for(resource_name)
     root_path
   end
diff --git a/app/controllers/plans_controller.rb b/app/controllers/plans_controller.rb
index 2a5514e..ad44829 100644
--- a/app/controllers/plans_controller.rb
+++ b/app/controllers/plans_controller.rb
@@ -162,19 +162,9 @@
 
     plan, phase = Plan.load_for_phase(params[:id], params[:phase_id])
 
-    readonly = !plan.editable_by?(current_user.id)
-
     guidance_groups =  GuidanceGroup.where(published: true, id: plan.guidance_group_ids)
-    # Since the answers have been pre-fetched through plan (see Plan.load_for_phase)
-    # we create a hash whose keys are question id and value is the answer associated
-    answers = plan.answers.reduce({}){ |m, a| m[a.question_id] = a; m }
 
-    render('/phases/edit', locals: {
-      base_template_org: phase.template.base_org,
-      plan: plan, phase: phase, readonly: readonly,
-      guidance_groups: guidance_groups,
-      answers: answers,
-      guidance_service: GuidanceService.new(plan) })
+    render_phases_edit(plan, phase, guidance_groups)
   end
 
   # PUT /plans/1
@@ -196,13 +186,13 @@
           format.json {render json: {code: 1, msg: success_message(_('plan'), _('saved'))}}
         else
           flash[:alert] = failed_update_error(@plan, _('plan'))
-          format.html { render action: "edit" }
+          format.html { render_phases_edit(@plan, @plan.phases.first, @plan.guidance_groups) }
           format.json {render json: {code: 0, msg: flash[:alert]}}
         end
 
       rescue Exception
         flash[:alert] = failed_update_error(@plan, _('plan'))
-        format.html { render action: "edit" }
+        format.html { render_phases_edit(@plan, @plan.phases.first, @plan.guidance_groups) }
         format.json {render json: {code: 0, msg: flash[:alert]}}
       end
     end
@@ -263,9 +253,13 @@
     @plan = Plan.includes(:answers).find(params[:id])
     authorize @plan
 
+    @selected_phase = @plan.phases.find(params[:phase_id])
+
     @show_coversheet = params[:export][:project_details].present?
     @show_sections_questions = params[:export][:question_headings].present?
     @show_unanswered = params[:export][:unanswered_questions].present?
+    @show_custom_sections = params[:export][:custom_sections].present?
+
     @public_plan = false
 
     @hash = @plan.as_pdf(@show_coversheet)
@@ -275,7 +269,7 @@
 
     respond_to do |format|
       format.html { render layout: false }
-      format.csv  { send_data @plan.as_csv(@show_sections_questions),  filename: "#{file_name}.csv" }
+      format.csv  { send_data @plan.as_csv(@show_sections_questions, @show_unanswered, @selected_phase, @show_custom_sections),  filename: "#{file_name}.csv" }
       format.text { send_data render_to_string(partial: 'shared/export/plan_txt'), filename: "#{file_name}.txt" }
       format.docx { render docx: "#{file_name}.docx", content: render_to_string(partial: 'shared/export/plan') }
       format.pdf do
@@ -431,7 +425,7 @@
 
   # Flash notice for successful feedback requests
   #
-  # @return [String]
+  # Returns String
   def request_feedback_flash_notice
     # Use the generic feedback confirmation message unless the Org has
     # specified one
@@ -439,4 +433,23 @@
              feedback_confirmation_default_message
     feedback_constant_to_text(text, current_user, @plan, current_user.org)
   end
+
+  private
+
+  # ============================
+  # = Private instance methods =
+  # ============================
+
+  def render_phases_edit(plan, phase, guidance_groups)
+    readonly = !plan.editable_by?(current_user.id)
+    # Since the answers have been pre-fetched through plan (see Plan.load_for_phase)
+    # we create a hash whose keys are question id and value is the answer associated
+    answers = plan.answers.reduce({}){ |m, a| m[a.question_id] = a; m }
+    render('/phases/edit', locals: {
+      base_template_org: phase.template.base_org,
+      plan: plan, phase: phase, readonly: readonly,
+      guidance_groups: guidance_groups,
+      answers: answers,
+      guidance_service: GuidanceService.new(plan) })
+  end
 end
diff --git a/app/controllers/registrations_controller.rb b/app/controllers/registrations_controller.rb
index f578bb7..0231a97 100644
--- a/app/controllers/registrations_controller.rb
+++ b/app/controllers/registrations_controller.rb
@@ -5,8 +5,8 @@
     @user = current_user
     @prefs = @user.get_preferences(:email)
     @languages = Language.sorted_by_abbreviation
-    @orgs = Org.where(parent_id: nil).order("name")
-    @other_organisations = Org.where(parent_id: nil, is_other: true).pluck(:id)
+    @orgs = Org.order("name")
+    @other_organisations = Org.where(is_other: true).pluck(:id)
     @identifier_schemes = IdentifierScheme.where(active: true).order(:name)
     @default_org = current_user.org
 
@@ -102,9 +102,9 @@
   def update
     if user_signed_in? then
       @prefs = @user.get_preferences(:email)
-      @orgs = Org.where(parent_id: nil).order("name")
+      @orgs = Org.order("name")
       @default_org = current_user.org
-      @other_organisations = Org.where(parent_id: nil, is_other: true).pluck(:id)
+      @other_organisations = Org.where(is_other: true).pluck(:id)
       @identifier_schemes = IdentifierScheme.where(active: true).order(:name)
       @languages = Language.sorted_by_abbreviation
       if params[:skip_personal_details] == "true"
diff --git a/app/controllers/super_admin/users_controller.rb b/app/controllers/super_admin/users_controller.rb
index c0640a3..9cddb77 100644
--- a/app/controllers/super_admin/users_controller.rb
+++ b/app/controllers/super_admin/users_controller.rb
@@ -8,37 +8,37 @@
       if user.present?
         authorize user
         languages = Language.sorted_by_abbreviation
-        orgs = Org.where(parent_id: nil).order("name")
+        orgs = Org.order("name")
         identifier_schemes = IdentifierScheme.where(active: true).order(:name)
-      
-        render 'super_admin/users/edit', 
-               locals: { user: user, 
+
+        render 'super_admin/users/edit',
+               locals: { user: user,
                          languages: languages,
-                         orgs: orgs, 
-                         identifier_schemes: identifier_schemes, 
+                         orgs: orgs,
+                         identifier_schemes: identifier_schemes,
                          default_org: user.org }
       else
         redirect_to admin_index_users_path, alert: _('User not found.')
       end
     end
-   
+
     def update
       user = User.find(params[:id])
       if user.present?
         authorize user
         topic = _('%{username}\'s profile') % { username: user.name(false) }
         if user.update_attributes(user_params)
-          redirect_to edit_super_admin_user_path(user), 
+          redirect_to edit_super_admin_user_path(user),
                       notice: _('Successfully updated %{username}') % { username: topic }
         else
-          redirect_to edit_super_admin_user_path(user), 
+          redirect_to edit_super_admin_user_path(user),
                       alert: _('Unable to update %{username}') % { username: topic }
         end
       else
         redirect_to edit_super_admin_user_path(user), alert: _('User not found.')
       end
     end
-     
+
     private
       def user_params
         params.require(:user).permit(:email, :firstname, :surname, :org_id, :language_id, :other_organisation)
diff --git a/app/controllers/users/omniauth_callbacks_controller.rb b/app/controllers/users/omniauth_callbacks_controller.rb
index 38719f9..c9aa43e 100644
--- a/app/controllers/users/omniauth_callbacks_controller.rb
+++ b/app/controllers/users/omniauth_callbacks_controller.rb
@@ -8,27 +8,26 @@
       handle_omniauth(scheme)
     end
   end
-  
-  ##
-  # Processes callbacks from an omniauth provider and directs the user to 
+
+  # Processes callbacks from an omniauth provider and directs the user to
   # the appropriate page:
   #   Not logged in and uid had no match ---> Sign Up page
   #   Not logged in and uid had a match ---> Sign In and go to Home Page
   #   Signed in and uid had no match --> Save the uid and go to the Profile Page
   #   Signed in and uid had a match --> Go to the Home Page
   #
-  # @scheme [IdentifierScheme] The IdentifierScheme for the provider
-  # -------------------------------------------------------------
+  # scheme - The IdentifierScheme for the provider
+  #
   def handle_omniauth(scheme)
     user = User.from_omniauth(request.env["omniauth.auth"].nil? ? request.env : request.env["omniauth.auth"])
-    
+
     # If the user isn't logged in
-    if current_user.nil? 
+    if current_user.nil?
       # If the uid didn't have a match in the system send them to register
       if user.nil?
         session["devise.#{scheme.name.downcase}_data"] = request.env["omniauth.auth"]
         redirect_to new_user_registration_url
-        
+
       # Otherwise sign them in
       else
         # Until ORCID becomes supported as a login method
@@ -40,20 +39,20 @@
           redirect_to new_user_registration_url
         end
       end
-      
+
     # The user is already logged in and just registering the uid with us
     else
       # If the user could not be found by that uid then attach it to their record
       if user.nil?
-        if UserIdentifier.create(identifier_scheme: scheme, 
+        if UserIdentifier.create(identifier_scheme: scheme,
                                  identifier: request.env["omniauth.auth"].uid,
                                  user: current_user)
-                               
+
           flash[:notice] = _('Your account has been successfully linked to %{scheme}.') % { scheme: scheme.description }
         else
           flash[:alert] = _('Unable to link your account to %{scheme}.') % { scheme: scheme.description }
         end
-        
+
       else
         # If a user was found but does NOT match the current user then the identifier has
         # already been attached to another account (likely the user has 2 accounts)
@@ -61,8 +60,8 @@
         if identifier.user.id != current_user.id
           flash[:alert] =  _("The current #{scheme.description} iD has been already linked to a user with email #{identifier.user.email}")
         end
-        
-        # Otherwise, the identifier was found and it matches the one already associated 
+
+        # Otherwise, the identifier was found and it matches the one already associated
         # with the current user so nothing else needs to be done
       end
 
@@ -71,7 +70,6 @@
     end
   end
 
-  # -------------------------------------------------------------
   def failure
     redirect_to root_path
   end
diff --git a/app/helpers/notifications_helper.rb b/app/helpers/notifications_helper.rb
index 9ee9a66..34d20de 100644
--- a/app/helpers/notifications_helper.rb
+++ b/app/helpers/notifications_helper.rb
@@ -1,6 +1,8 @@
 module NotificationsHelper
-  # Return FA html class depending on Notification level
-  # @return [String] Font Awesome HTML class
+
+  # FA html class depending on Notification level
+  #
+  # Returns String
   def fa_classes(notification)
     case notification.level
     when 'warning'
diff --git a/app/helpers/orgs_helper.rb b/app/helpers/orgs_helper.rb
index f106fa1..a2be874 100644
--- a/app/helpers/orgs_helper.rb
+++ b/app/helpers/orgs_helper.rb
@@ -1,12 +1,14 @@
+# frozen_string_literal: true
+
 module OrgsHelper
-  # frozen_string_literal: true
 
   DEFAULT_EMAIL = '%{organisation_email}'
 
   # Tooltip string for Org feedback form.
   #
-  # @param org [Org] The current Org we're updating feedback form for.
-  # @return [String] The tooltip message
+  # org - The current Org we're updating feedback form for.
+  #
+  # Returns String
   def tooltip_for_org_feedback_form(org)
     email = org.contact_email.presence || DEFAULT_EMAIL
     _("SAMPLE MESSAGE: A data librarian from %{org_name} will respond to your request within 48
diff --git a/app/helpers/plans_helper.rb b/app/helpers/plans_helper.rb
index b726508..f761b11 100644
--- a/app/helpers/plans_helper.rb
+++ b/app/helpers/plans_helper.rb
@@ -42,4 +42,15 @@
       return _('Private: restricted to me and people I invite.')
     end
   end
+
+  def download_plan_page_title(plan, phase, hash)
+    # If there is more than one phase show the plan title and phase title
+    return hash[:phases].many? ? "#{plan.title} - #{phase[:title]}" : plan.title
+  end
+  
+  def display_questions_and_section_headings(section, show_sections_questions, show_custom_sections)
+    # Return true if show_sections_questions is true and either section not customised, or section is customised
+    # and show_custom_sections is true
+    return show_sections_questions && (!section[:modifiable] || (show_custom_sections && section[:modifiable]))
+  end
 end
diff --git a/app/helpers/sections_helper.rb b/app/helpers/sections_helper.rb
index 785b6b1..6b16842 100644
--- a/app/helpers/sections_helper.rb
+++ b/app/helpers/sections_helper.rb
@@ -2,11 +2,11 @@
   # HREF attribute value for headers in the section partials. If the section
   # is modifiable, returns the section path, otherwise the edit section path.
   #
-  # @param section [Section] The section to return a URL for
-  # @param phase [Phase] The phase that section belongs
-  # @param template [Template] The template that phase belongs to
+  # section  - The section to return a URL for
+  # phase    - The phase that section belongs
+  # template - The template that phase belongs to
   #
-  # @return String
+  # Returns String
   def header_path_for_section(section, phase, template)
     if section.modifiable?
       edit_org_admin_template_phase_section_path(template_id: template.id,
diff --git a/app/mailers/user_mailer.rb b/app/mailers/user_mailer.rb
index d459b3e..525773b 100644
--- a/app/mailers/user_mailer.rb
+++ b/app/mailers/user_mailer.rb
@@ -108,8 +108,8 @@
     end
   end
 
-  # @param commenter - User who wrote the comment
-  # @param plan - Plan for which the comment is associated to
+  # commenter - User who wrote the comment
+  # plan      - Plan for which the comment is associated to
   def new_comment(commenter, plan)
     if commenter.is_a?(User) && plan.is_a?(Plan)
       owner = plan.owner
diff --git a/app/models/annotation.rb b/app/models/annotation.rb
index 5cad46d..6c7d7b5 100644
--- a/app/models/annotation.rb
+++ b/app/models/annotation.rb
@@ -58,11 +58,11 @@
   # = Class Methods =
   # =================
 
-  ##
-  # deep copy the given annotation and all it's associations
+  # Deep copy the given annotation and all it's associations
   #
-  # @params [Annotation] annotation to be deep copied
-  # @return [Annotation] the saved, copied annotation
+  # annotation - To be deep copied
+  #
+  # Returns Annotation
   def self.deep_copy(annotation)
     annotation_copy = annotation.dup
     annotation_copy.save!
@@ -73,10 +73,9 @@
   # = Public instance methods =
   # ===========================
 
-  ##
-  # returns the text from the annotation
+  # The text from the annotation
   #
-  # @return [String] the text from the annotation
+  # Returns String
   def to_s
     "#{text}"
   end
diff --git a/app/models/answer.rb b/app/models/answer.rb
index 22b9a09..738dc5d 100644
--- a/app/models/answer.rb
+++ b/app/models/answer.rb
@@ -65,8 +65,9 @@
   ##
   # deep copy the given answer
   #
-  # @params [Answer] question_option to be deep copied
-  # @return [Answer] the saved, copied answer
+  # answer - question_option to be deep copied
+  #
+  # Returns Answer
   def self.deep_copy(answer)
     answer_copy = answer.dup
     answer.question_options.each do |opt|
@@ -75,14 +76,19 @@
     answer_copy
   end
 
-  # This method helps to decide if an answer option (:radiobuttons, :checkbox, etc ) in form views should be checked or not
-  # Returns true if the given option_id is present in question_options, otherwise returns false
+  # This method helps to decide if an answer option (:radiobuttons, :checkbox, etc ) in
+  # form views should be checked or not
+  #
+  # Returns Boolean
   def has_question_option(option_id)
     self.question_option_ids.include?(option_id)
   end
 
-  # Returns true if the answer is valid and false otherwise. If the answer's question is option_based, it is checked if exist
-  # any question_option selected. For non option_based (e.g. textarea or textfield), it is checked the presence of text
+  # If the answer's question is option_based, it is checked if exist any question_option
+  # selected. For non option_based (e.g. textarea or textfield), it is checked the
+  # presence of text
+  #
+  # Returns Boolean
   def is_valid?
     if self.question.present?
       if self.question.question_format.option_based?
@@ -94,16 +100,17 @@
     return false
   end
 
-  # Returns answer notes whose archived is blank sorted by updated_at in descending order
+  # Answer notes whose archived is blank sorted by updated_at in descending order
+  #
+  # Returns Array
   def non_archived_notes
     return notes.select{ |n| n.archived.blank? }.sort!{ |x,y| y.updated_at <=> x.updated_at }
   end
 
-  ##
-  # Returns True if answer text is blank, false otherwise
-  # specificly we want to remove empty hml tags and check
+  # Returns True if answer text is blank, false otherwise specificly we want to remove
+  # empty hml tags and check.
   #
-  # @return [Boolean] is the answer's text blank
+  # Returns Boolean
   def is_blank?
     if self.text.present?
       return self.text.gsub(/<\/?p>/, '').gsub(/<br\s?\/?>/, '').chomp.blank?
@@ -112,14 +119,10 @@
     return true
   end
 
-  ##
-  # Returns the parsed JSON hash for the current answer object
-  # Generates a new hash if none exists for rda_questions
+  # The parsed JSON hash for the current answer object. Generates a new hash if none
+  # exists for rda_questions.
   #
-  # @return [Hash] the parsed hash of the answer.
-  #                Should have keys 'standards', 'text'
-  #                'standards' is a list of <std_id>: <title> pairs
-  #                'text' is the text from the comments box
+  # Returns Hash
   def answer_hash
     default = {'standards' => {}, 'text' => ''}
     begin
@@ -131,12 +134,13 @@
   end
 
   ##
-  # Given a hash of standards and a comment value, this updates answer
-  # text for rda_questions
+  # Given a hash of standards and a comment value, this updates answer text for
+  # rda_questions
   #
-  # @param [standards] a hash of standards
-  # @param [text]  option comment text
-  # nothing returned, but the status of the text field of the answer is changed
+  # standards - A Hash of standards
+  # text      - A String with option comment text
+  #
+  # Returns String
   def update_answer_hash(standards={},text="")
     h = {}
     h['standards'] = standards
diff --git a/app/models/concerns/exportable_plan.rb b/app/models/concerns/exportable_plan.rb
index 37af160..6a6fdde 100644
--- a/app/models/concerns/exportable_plan.rb
+++ b/app/models/concerns/exportable_plan.rb
@@ -4,11 +4,11 @@
     prepare(coversheet)
   end
 
-  def as_csv(headings = true, unanswered = true)
+  def as_csv(headings = true, unanswered = true, selected_phase = nil, show_custom_sections = true)
     hash = prepare(false)
 
     CSV.generate do |csv|
-      hdrs = (hash[:phases].length > 1 ? [_('Phase')] : [])
+      hdrs = (hash[:phases].many? ? [_('Phase')] : [])
       if headings
         hdrs << [_('Section'),_('Question'),_('Answer')]
       else
@@ -17,23 +17,30 @@
 
       csv << hdrs.flatten
       hash[:phases].each do |phase|
-        phase[:sections].each do |section|
-          section[:questions].each do |question|
-            answer = self.answer(question[:id], false)
-            answer_text = answer.present? ? answer.text : (unanswered ? _('Not Answered') : '')
-            flds = (hash[:phases].length > 1 ? [phase[:title]] : [])
-            if headings
-              if question[:text].is_a? String
-                question_text = question[:text]
-              else
-                question_text = (question[:text].length > 1 ? question[:text].join(', ') : question[:text][0])
+        if  selected_phase.nil? || phase[:title] == selected_phase.title
+          phase[:sections].each do |section|
+            # Return true if either section not customised, or section is customised
+            # and unanswered is true
+            if !section[:modifiable] || (show_custom_sections && section[:modifiable])
+              section[:questions].each do |question|
+                answer = self.answer(question[:id], false)
+                if answer.present? || (answer.blank? && unanswered)
+                  answer_text = answer.present? ? answer.text : (unanswered ? _('Not Answered') : '')
+                  flds = (hash[:phases].many? ? [phase[:title]] : [])
+                  if headings
+                    if question[:text].is_a? String
+                      question_text = question[:text]
+                    else
+                      question_text = (question[:text].many? ? question[:text].join(', ') : question[:text][0])
+                    end
+                    flds << [ section[:title], sanitize_text(question_text), sanitize_text(answer_text) ]
+                  else
+                    flds << [ sanitize_text(answer_text) ]
+                  end
+                  csv << flds.flatten
+                end
               end
-              flds << [ section[:title], sanitize_text(question_text), sanitize_text(answer_text) ]
-            else
-              flds << [ sanitize_text(answer_text) ]
             end
-
-            csv << flds.flatten
           end
         end
       end
@@ -56,7 +63,7 @@
     template.phases.each do |phase|
       phs = { title: phase.title, number: phase.number, sections: [] }
       phase.sections.each do |section|
-        sctn = { title: section.title, number: section.number, questions: [] }
+        sctn = { title: section.title, number: section.number, questions: [], modifiable: section.modifiable }
         section.questions.each do |question|
           txt = question.text
           sctn[:questions] << { id: question.id, text: txt, format: question.question_format }
diff --git a/app/models/guidance.rb b/app/models/guidance.rb
index 4258326..602e7ad 100644
--- a/app/models/guidance.rb
+++ b/app/models/guidance.rb
@@ -12,7 +12,6 @@
 #  created_at        :datetime         not null
 #  updated_at        :datetime         not null
 #  guidance_group_id :integer
-#  question_id       :integer
 #
 # Indexes
 #
@@ -72,17 +71,16 @@
   # = Class methods =
   # =================
 
-  ##
   # Returns whether or not a given user can view a given guidance
   # we define guidances viewable to a user by those owned by a guidance group:
   #   owned by the managing curation center
   #   owned by a funder organisation
   #   owned by an organisation, of which the user is a member
   #
-  # @param id [Integer] the integer id for a guidance
-  # @param user [User] a user object
-  # @return [Boolean] true if the specified user can view the specified
-  # guidance, false otherwise
+  # id   - The Integer id for a guidance
+  # user - A User object
+  #
+  # Returns Boolean
   def self.can_view?(user, id)
     guidance = Guidance.find_by(id: id)
     viewable = false
@@ -109,15 +107,15 @@
     return viewable
   end
 
-  ##
   # Returns a list of all guidances which a specified user can view
   # we define guidances viewable to a user by those owned by a guidance group:
   #   owned by the Managing Curation Center
   #   owned by a funder organisation
   #   owned by an organisation, of which the user is a member
   #
-  # @param user [User] a user object
-  # @return [Array<Guidance>] a list of all "viewable" guidances to a user
+  # user - A User object
+  #
+  # Returns Array
   def self.all_viewable(user)
     managing_groups = Org.includes(guidance_groups: :guidances)
                          .managing_orgs.collect{|o| o.guidance_groups}
@@ -138,13 +136,12 @@
     return all_viewable_guidances.flatten
   end
 
-  ##
   # Determine if a guidance is in a group which belongs to a specified
   # organisation
   #
-  # @param org_id [Integer] the integer id for an organisation
-  # @return [Boolean] true if this guidance is in a group belonging to the
-  # specified organisation, false otherwise
+  # org_id - The Integer id for an organisation
+  #
+  # Returns Boolean
   def in_group_belonging_to?(org_id)
     unless guidance_group.nil?
       if guidance_group.org.id == org_id
diff --git a/app/models/guidance_group.rb b/app/models/guidance_group.rb
index 36d780d..3a63430 100644
--- a/app/models/guidance_group.rb
+++ b/app/models/guidance_group.rb
@@ -21,6 +21,7 @@
 #
 #  fk_rails_...  (org_id => orgs.id)
 #
+
 class GuidanceGroup < ActiveRecord::Base
   include GlobalHelpers
   include ValidationValues
@@ -70,17 +71,16 @@
   # = Class methods =
   # =================
 
-  ##
-  # Returns whether or not a given user can view a given guidance group
+  # Whether or not a given user can view a given guidance group
   # we define guidances viewable to a user by those owned by:
   #   the managing curation center
   #   a funder organisation
   #   an organisation, of which the user is a member
   #
-  # @param id [Integer] the integer id for a guidance group
-  # @param user [User] a user object
-  # @return [Boolean] true if the specified user can view the specified
-  # guidance group, false otherwise
+  # id   - The integer id for a guidance group
+  # user - A User object
+  #
+  # Returns Boolean
   def self.can_view?(user, guidance_group)
     viewable = false
     # groups are viewable if they are owned by any of the user's organisations
@@ -95,16 +95,16 @@
     viewable
   end
 
-  ##
-  # Returns a list of all guidance groups which a specified user can view
+
+  # A list of all guidance groups which a specified user can view
   # we define guidance groups viewable to a user by those owned by:
   #   the Managing Curation Center
   #   a funder organisation
   #   an organisation, of which the user is a member
   #
-  # @param user [User] a user object
-  # @return [Array<GuidanceGroup>] a list of all "viewable" guidance groups to
-  # a user
+  # user - A User object
+  #
+  # Returns Array
   def self.all_viewable(user)
     # first find all groups owned by the Managing Curation Center
     managing_org_groups = Org.includes(guidance_groups: [guidances: :themes])
@@ -118,7 +118,7 @@
     organisation_groups = [user.org.guidance_groups]
 
     # pass this organisation guidance groups to the view with respond_with
-    # @all_viewable_groups
+    # all_viewable_groups
     all_viewable_groups = managing_org_groups +
                           funder_groups +
                           organisation_groups
diff --git a/app/models/notification.rb b/app/models/notification.rb
index b5a6962..dd6a17d 100644
--- a/app/models/notification.rb
+++ b/app/models/notification.rb
@@ -69,7 +69,8 @@
 
   # Has the Notification been acknowledged by the given user ?
   # If no user is given, currently logged in user (if any) is the default
-  # @return [Boolean] is the Notification acknowledged ?
+  #
+  # Returns Boolean
   def acknowledged?(user)
     dismissable? && user.present? && users.include?(user)
   end
diff --git a/app/models/org.rb b/app/models/org.rb
index 881f990..f97042c 100644
--- a/app/models/org.rb
+++ b/app/models/org.rb
@@ -4,7 +4,6 @@
 #
 #  id                     :integer          not null, primary key
 #  abbreviation           :string
-#  banner_text            :text
 #  contact_email          :string
 #  contact_name           :string
 #  feedback_email_msg     :text
@@ -12,18 +11,15 @@
 #  feedback_enabled       :boolean          default(FALSE)
 #  is_other               :boolean          default(FALSE), not null
 #  links                  :text
-#  logo_file_name         :string
 #  logo_name              :string
 #  logo_uid               :string
 #  name                   :string
 #  org_type               :integer          default(0), not null
 #  sort_name              :string
 #  target_url             :string
-#  wayfless_entity        :string
 #  created_at             :datetime         not null
 #  updated_at             :datetime         not null
 #  language_id            :integer
-#  parent_id              :integer
 #  region_id              :integer
 #
 # Foreign Keys
@@ -137,7 +133,9 @@
   # What do they do? do they do it efficiently, and do we need them?
 
   # Determines the locale set for the organisation
-  # @return String or nil
+  #
+  # Returns String
+  # Returns nil
   def get_locale
     if !self.language.nil?
       return self.language.abbreviation
@@ -146,16 +144,14 @@
     end
   end
 
-# TODO: Should these be hardcoded? Also, an Org can currently be multiple org_types at one time.
-#       For example you can do: funder = true; project = true; school = true
-#       Calling type in the above scenario returns "Funder" which is a bit misleading
-#       Is FlagShihTzu's Bit flag the appropriate structure here or should we use an enum?
-#       Tests are setup currently to work with this issue.
-  ##
-  # returns the name of the type of the organisation as a string
-  # defaults to none if no org type present
+  # TODO: Should these be hardcoded? Also, an Org can currently be multiple org_types at
+  # one time. For example you can do: funder = true; project = true; school = true
   #
-  # @return [String]
+  # Calling type in the above scenario returns "Funder" which is a bit misleading
+  # Is FlagShihTzu's Bit flag the appropriate structure here or should we use an enum?
+  # Tests are setup currently to work with this issue.
+  #
+  # Returns String
   def org_type_to_s
     ret = []
     ret << "Institution" if self.institution?
@@ -172,17 +168,17 @@
   end
 
   ##
-  # returns the name of the organisation
+  # The name of the organisation
   #
-  # @return [String]
+  # Returns String
   def to_s
     name
   end
 
   ##
-  # returns the abbreviation for the organisation if it exists, or the name if not
+  # The abbreviation for the organisation if it exists, or the name if not
   #
-  # @return [String] name or abbreviation of the organisation
+  # Returns String
   def short_name
     if abbreviation.nil? then
       return name
@@ -192,9 +188,9 @@
   end
 
   ##
-  # returns all published templates belonging to the organisation
+  # All published templates belonging to the organisation
   #
-  # @return [Array<Template>] published templates
+  # Returns ActiveRecord::Relation
   def published_templates
     return templates.where("published = ?", true)
   end
diff --git a/app/models/phase.rb b/app/models/phase.rb
index 41a985b..58a466d 100644
--- a/app/models/phase.rb
+++ b/app/models/phase.rb
@@ -6,7 +6,6 @@
 #  description :text
 #  modifiable  :boolean
 #  number      :integer
-#  slug        :string
 #  title       :string
 #  created_at  :datetime
 #  updated_at  :datetime
diff --git a/app/models/plan.rb b/app/models/plan.rb
index 04e7642..434cbbe 100644
--- a/app/models/plan.rb
+++ b/app/models/plan.rb
@@ -21,7 +21,6 @@
 #  principal_investigator_email      :string
 #  principal_investigator_identifier :string
 #  principal_investigator_phone      :string
-#  slug                              :string
 #  title                             :string
 #  visibility                        :integer          default(3), not null
 #  created_at                        :datetime
@@ -36,6 +35,7 @@
 #
 #  fk_rails_...  (template_id => templates.id)
 #
+
 class Plan < ActiveRecord::Base
   include ConditionalUserMailer
   include ExportablePlan
@@ -194,8 +194,9 @@
 
   # deep copy the given plan and all of it's associations
   #
-  # @params [Plan] plan to be deep copied
-  # @return [Plan] saved copied plan
+  # plan - Plan to be deep copied
+  #
+  # Returns Plan
   def self.deep_copy(plan)
     plan_copy = plan.dup
     plan_copy.title = "Copy of " + plan.title
@@ -229,15 +230,15 @@
     template&.settings(key)
   end
 
-  ##
-  # returns the most recent answer to the given question id
-  # optionally can create an answer if none exists
+  # The most recent answer to the given question id optionally can create an answer if
+  # none exists.
   #
-  # @param qid [Integer] the id for the question to find the answer for
-  # @param create_if_missing [Boolean] if true, will genereate a default answer
-  # to the question.
-  # @return [Answer,nil] the most recent answer to the question, or a new
-  # question with default value, or nil.
+  # qid               - The id for the question to find the answer for
+  # create_if_missing - If true, will genereate a default answer
+  #                     to the question (defaults: true).
+  #
+  # Returns Answer
+  # Returns nil
   def answer(qid, create_if_missing = true)
     answer = answers.where(question_id: qid).order("created_at DESC").first
     question = Question.find(qid)
@@ -331,8 +332,9 @@
   ##
   # determines if the plan is editable by the specified user
   #
-  # @param user_id [Integer] the id for a user
-  # @return [Boolean] true if user can edit the plan
+  # user_id - The id for a user
+  #
+  # Returns Boolean
   def editable_by?(user_id)
     user_id = user_id.id if user_id.is_a?(User)
     role?(user_id, :editor)
@@ -341,8 +343,9 @@
   ##
   # determines if the plan is readable by the specified user
   #
-  # @param user_id [Integer] the id for a user
-  # @return [Boolean] true if the user can read the plan
+  # user_id - The Integer id for a user
+  #
+  # Returns Boolean
   def readable_by?(user_id)
     user           = user_id.is_a?(User) ? user_id : User.find(user_id)
     owner_orgs     = owner_and_coowners.collect(&:org)
@@ -363,58 +366,57 @@
     false
   end
 
-  ##
-  # determines if the plan is readable by the specified user
+  # determines if the plan is readable by the specified user.
   #
-  # @param user_id [Integer] the id for a user
-  # @return [Boolean] true if the user can read the plan
+  # user_id - The Integer id for a user
+  #
+  # Returns Boolean
   def commentable_by?(user_id)
     user_id = user_id.id if user_id.is_a?(User)
     role?(user_id, :commenter)
   end
 
-  ##
   # determines if the plan is administerable by the specified user
   #
-  # @param user_id [Integer] the id for the user
-  # @return [Boolean] true if the user can administer the plan
+  # user_id - The Integer id for the user
+  #
+  # Returns Boolean
   def administerable_by?(user_id)
     user_id = user_id.id if user_id.is_a?(User)
     role?(user_id, :administrator)
   end
 
-  ##
   # determines if the plan is reviewable by the specified user
   #
-  # @param user_id [Integer] the id for the user
-  # @return [Boolean] true if the user can administer the plan
+  # user_id - The Integer id for the user
+  #
+  # Returns Boolean
   def reviewable_by?(user_id)
     user_id = user_id.id if user_id.is_a?(User)
     role?(user_id, :reviewer)
   end
 
-  ##
   # Assigns the passed user_id to the creater_role for the project gives the
   # user rights to read, edit, administrate, and defines them as creator
   #
-  # @param user_id [Integer] the user to be given priveleges' id
+  # user_id - The Integer user to be given priveleges' id
+  #
   def assign_creator(user_id)
     user_id = user_id.id if user_id.is_a?(User)
     add_user(user_id, true, true, true)
   end
 
-  ##
   # the datetime for the latest update of this plan
   #
-  # @return [DateTime] the time of latest update
+  # Returns DateTime
   def latest_update
     (phases.pluck(:updated_at) + [updated_at]).max
   end
 
-  ##
   # the owner of the project
   #
-  # @return [User] the creater of the project
+  # Returns User
+  # Returns nil
   def owner
     vals = Role.access_values_for(:creator)
     User.joins(:roles)
@@ -424,7 +426,7 @@
   ##
   # TODO: Rewrite this description
   #
-  # returns the shared roles of a plan, excluding the creator
+  # Returns Boolean
   def shared?
     roles.where(Role.not_creator_condition).any?
   end
@@ -433,10 +435,9 @@
 
   deprecate :shared, deprecator: Cleanup::Deprecators::PredicateDeprecator.new
 
-  ##
   # the owner and co-owners of the project
   #
-  # @return [Users]
+  # Returns ActiveRecord::Relation
   def owner_and_coowners
     vals = Role.access_values_for(:creator)
                .concat(Role.access_values_for(:administrator))
@@ -444,7 +445,9 @@
         .where(roles: { plan_id: id, access: vals })
   end
 
-  # Returns the number of answered questions from the entire plan
+  # The number of answered questions from the entire plan
+  #
+  # Returns Integer
   def num_answered_questions
     Answer.where(id: answers.map(&:id))
           .includes(:question_options, { question: :question_format })
@@ -452,7 +455,9 @@
           .sum { |answer| answer.is_valid? ? 1 : 0 }
   end
 
-  # Returns the number of questions for a plan.
+  # The number of questions for a plan.
+  #
+  # Returns Integer
   def num_questions
     questions.count
   end
@@ -460,6 +465,8 @@
   # Determines whether or not visibility changes are permitted according to the
   # percentage of the plan answered in respect to a threshold defined at
   # application.config
+  #
+  # Returns Boolean
   def visibility_allowed?
     value=(num_answered_questions.to_f/num_questions*100).round(2)
     !is_test? && value >= Rails.application
@@ -468,12 +475,16 @@
   end
 
   # Determines whether or not a question (given its id) exists for the self plan
+  #
+  # Returns Boolean
   def question_exists?(question_id)
     Plan.joins(:questions).exists?(id: id, "questions.id": question_id)
   end
 
   # Checks whether or not the number of questions matches the number of valid
   # answers
+  #
+  # Returns Boolean
   def no_questions_matches_no_answers?
     num_questions = question_ids.length
     pre_fetched_answers = Answer.includes(:question_options,
@@ -502,19 +513,18 @@
 
   deprecate :has_role, deprecator: Cleanup::Deprecators::PredicateDeprecator.new
 
-  ##
-  # adds a user to the project
-  # if no flags are specified, the user is given read privleges
-  #
-  # @param user_id [Integer] the user to be given privleges
-  # @param is_editor [Boolean] whether or not the user can edit the project
-  # @param is_administrator [Boolean] whether or not the user can administrate
-  # the project
-  # @param is_creator [Boolean] wheter or not the user created the project
-  # @return [Array<ProjectGroup>]
-  #
+  # Adds a user to the project if no flags are specified, the user is given read privleges
   # TODO: change this to specifying uniqueness of user/plan association and
-  # handle that way
+  # handle that way.
+  #
+  #
+  # user_id          - The Integer user ID to be given privleges
+  # is_editor        - Whether or not the user can edit the project (defaults: false)
+  # is_administrator - Whether or not the user can administrate the project
+  #                    (defaults: false)
+  # is_creator       - Wheter or not the user created the project (defaults: false)
+  #
+  # Returns Boolean
   #
   def add_user(user_id, is_editor = false,
                         is_administrator = false,
@@ -547,7 +557,9 @@
   end
 
   # Initialize the title for new templates
-  # --------------------------------------------------------
+  #
+  # Returns nil
+  # Returns String
   def set_creation_defaults
     # Only run this before_validation because rails fires this before
     # save/create
diff --git a/app/models/pref.rb b/app/models/pref.rb
index 22d8bfc..c3c4707 100644
--- a/app/models/pref.rb
+++ b/app/models/pref.rb
@@ -28,10 +28,9 @@
 
   validates :settings, presence: { message: PRESENCE_MESSAGE }
 
-  ##
-  # Returns the hash generated from default preferences
+  # The default preferences
   #
-  # @return [JSON] preferences hash
+  # Returns Hash
   def self.default_settings
     Branding.fetch(:preferences)
   end
diff --git a/app/models/question.rb b/app/models/question.rb
index 2a1027d..8b36f9a 100644
--- a/app/models/question.rb
+++ b/app/models/question.rb
@@ -117,8 +117,9 @@
   # This method doesn't even make reference to this class and its returning
   # a hash that is specific to a view guidance for org
   #
-  # @param org [Org] the org to find guidance for
-  # @return [Hash{String => String}]
+  # org - The Org to find guidance for
+  #
+  # Returns Hash
   def guidance_for_org(org)
     # pulls together guidance from various sources for question
     guidances = {}
@@ -138,11 +139,11 @@
     return guidances
    end
 
-  ##
   # get example answer belonging to the currents user for this question
   #
-  # @param org_ids [Array<Integer>] the ids for the organisations
-  # @return [Array<Annotation>] the example answers for this question for the specified orgs
+  # org_ids - The ids for the organisations
+  #
+  # Returns ActiveRecord::Relation
    def example_answers(org_ids)
     annotations.where(org_id: Array(org_ids),
                       type: Annotation.types[:example_answer])
@@ -154,13 +155,12 @@
    deprecate :get_example_answers,
                deprecator: Cleanup::Deprecators::GetDeprecator.new
 
-  ##
   # get guidance belonging to the current user's org for this question(need org
   # to distinguish customizations)
   #
-  # @param org_id [Integer] the id for the organisation
-  # @return [String] the annotation guidance for this question for the
-  # specified org
+  # org_id - The id for the organisation
+  #
+  # Returns Annotation
   def guidance_annotation(org_id)
     annotations.where(org_id: org_id, type: Annotation.types[:guidance]).first
   end
diff --git a/app/models/role.rb b/app/models/role.rb
index db4ad6e..321aff3 100644
--- a/app/models/role.rb
+++ b/app/models/role.rb
@@ -102,9 +102,9 @@
   ##
   # Roles with given FlagShihTzu access flags
   #
-  # @param flags [Array] One or more symbols that represent access flags
+  # flags - One or more symbols that represent access flags
   #
-  # @return [ActiveRecord::Relation]
+  # Return ActiveRecord::Relation
   scope :with_access_flags, -> (*flags) {
     bad_flag = flags.detect { |flag| !flag.in?(flag_mapping['access'].keys) }
     raise ArgumentError, "Unkown access flag '#{bad_flag}'" if bad_flag
@@ -118,15 +118,15 @@
   # = Public instance methods =
   # ===========================
 
-  ##
-  # return the access level for the current project group
-  # 5 if the user is a reviewer
-  # 3 if the user is an administrator
-  # 2 if the user is an editor
-  # 1 if the user can only read
+
+  # The access level for the current project group:
+  # - 5 if the user is a reviewer
+  # - 3 if the user is an administrator
+  # - 2 if the user is an editor
+  # - 1 if the user can only read
   # used to facilliatte formtastic
   #
-  # @return [Integer]
+  # Returns Integer
   def access_level
     if self.reviewer?
       return 5
diff --git a/app/models/section.rb b/app/models/section.rb
index 0152f52..42cb330 100644
--- a/app/models/section.rb
+++ b/app/models/section.rb
@@ -74,24 +74,21 @@
 
   # The sections for this Phase that have been added by the admin
   #
-  # @!scope class
-  # @return [ActiveRecord::Relation] Returns the sections that are modifiable
+  # Returns ActiveRecord::Relation
   scope :modifiable, -> { where(modifiable: true) }
 
   # The sections for this Phase that were part of the original Template
   #
-  # @!scope class
-  # @return [ActiveRecord::Relation] Returns the sections that aren't modifiable
+  # Returns ActiveRecord::Relation
   scope :not_modifiable, -> { where(modifiable: false) }
 
   # ===========================
   # = Public instance methods =
   # ===========================
 
-  ##
-  # return the title of the section
+  # The title of the Section
   #
-  # @return [String] the title of the section
+  # Returns String
   def to_s
     "#{title}"
   end
diff --git a/app/models/theme.rb b/app/models/theme.rb
index 857ee30..4e66430 100644
--- a/app/models/theme.rb
+++ b/app/models/theme.rb
@@ -39,10 +39,9 @@
   # = Public instance methods =
   # ===========================
 
-  ##
-  # returns the title of the theme
+  # The title of the Theme
   #
-  # @return [String] title of the theme
+  # Returns String
   def to_s
   	title
   end
diff --git a/app/models/token_permission_type.rb b/app/models/token_permission_type.rb
index 8c75ee3..8dd979b 100644
--- a/app/models/token_permission_type.rb
+++ b/app/models/token_permission_type.rb
@@ -48,10 +48,9 @@
                          uniqueness: { message: UNIQUENESS_MESSAGE }
 
 
-  ##
-  # returns the token_type of the token_permission_type
+  # The token_type of the token_permission_type
   #
-  # @return [String] token_type of the token_permission_type
+  # Returns String
   def to_s
     self.token_type
   end
diff --git a/app/models/user.rb b/app/models/user.rb
index babd2fd..76882a7 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -32,9 +32,7 @@
 #  updated_at             :datetime         not null
 #  invited_by_id          :integer
 #  language_id            :integer
-#  orcid_id               :string
 #  org_id                 :integer
-#  shibboleth_id          :string
 #
 # Indexes
 #
@@ -152,8 +150,9 @@
   # = Public instance methods =
   # ===========================
 
-  ##
   # This method uses Devise's built-in handling for inactive users
+  #
+  # Returns Boolean
   def active_for_authentication?
     super && active?
   end
@@ -163,7 +162,9 @@
   # What do they do? do they do it efficiently, and do we need them?
 
   # Determines the locale set for the user or the organisation he/she belongs
-  # @return String or nil
+  #
+  # Returns String
+  # Returns nil
   def get_locale
     if !self.language.nil?
       return self.language.abbreviation
@@ -174,11 +175,11 @@
     end
   end
 
-  ##
-  # gives either the name of the user, or the email if name unspecified
+  # Gives either the name of the user, or the email if name unspecified
   #
-  # @param user_email [Boolean] defaults to true, allows the use of email if there is no firstname or surname
-  # @return [String] the email or the firstname and surname of the user
+  # user_email - Use the email if there is no firstname or surname (defaults: true)
+  #
+  # Returns String
   def name(use_email = true)
     if (firstname.blank? && surname.blank?) || use_email then
       return email
@@ -188,113 +189,103 @@
     end
   end
 
-  ##
-  # Returns the user's identifier for the specified scheme name
+  # The user's identifier for the specified scheme name
   #
-  # @param the identifier scheme name (e.g. ORCID)
-  # @return [UserIdentifier] the user's identifier for that scheme
+  # scheme - The identifier scheme name (e.g. ORCID)
+  #
+  # Returns UserIdentifier
   def identifier_for(scheme)
     user_identifiers.where(identifier_scheme: scheme).first
   end
 
-  ##
-  # checks if the user is a super admin
-  # if the user has any privelege which requires them to see the super admin page
-  # then they are a super admin
+  # Checks if the user is a super admin. If the user has any privelege which requires
+  # them to see the super admin page then they are a super admin.
   #
-  # @return [Boolean] true if the user is an admin
+  # Returns Boolean
   def can_super_admin?
     return self.can_add_orgs? || self.can_grant_api_to_orgs? || self.can_change_org?
   end
 
-  ##
-  # checks if the user is an organisation admin
-  # if the user has any privlege which requires them to see the org-admin pages
-  # then they are an org admin
+  # Checks if the user is an organisation admin if the user has any privlege which
+  # requires them to see the org-admin pages then they are an org admin.
   #
-  # @return [Boolean] true if the user is an organisation admin
+  # Returns Boolean
   def can_org_admin?
     return self.can_grant_permissions? || self.can_modify_guidance? ||
            self.can_modify_templates? || self.can_modify_org_details?
   end
 
-  ##
-  # checks if the user can add new organisations
+  # Can the User add new organisations?
   #
-  # @return [Boolean] true if the user can add new organisations
+  # Returns Boolean
   def can_add_orgs?
     perms.include? Perm.add_orgs
   end
 
-  ##
-  # checks if the user can change their organisation affiliations
+  # Can the User change their organisation affiliations?
   #
-  # @return [Boolean] true if the user can change their organisation affiliations
+  # Returns Boolean
   def can_change_org?
     perms.include? Perm.change_affiliation
   end
 
-  ##
-  # checks if the user can grant their permissions to others
+  # Can the User can grant their permissions to others?
   #
-  # @return [Boolean] true if the user can grant their permissions to others
+  # Returns Boolean
   def can_grant_permissions?
     perms.include? Perm.grant_permissions
   end
 
-  ##
-  # checks if the user can modify organisation templates
+  # Can the User modify organisation templates?
   #
-  # @return [Boolean] true if the user can modify organisation templates
+  # Returns Boolean
   def can_modify_templates?
     self.perms.include? Perm.modify_templates
   end
 
-  ##
-  # checks if the user can modify organisation guidance
+  # Can the User modify organisation guidance?
   #
-  # @return [Boolean] true if the user can modify organistion guidance
+  # Returns Boolean
   def can_modify_guidance?
     perms.include? Perm.modify_guidance
   end
 
-  ##
-  # checks if the user can use the api
+  # Can the User use the API?
   #
-  # @return [Boolean] true if the user can use the api
+  # Returns Boolean
   def can_use_api?
     perms.include? Perm.use_api
   end
 
-  ##
-  # checks if the user can modify their org's details
+  # Can the User modify their org's details?
   #
-  # @return [Boolean] true if the user can modify the org's details
+  # Returns Boolean
   def can_modify_org_details?
     perms.include? Perm.change_org_details
   end
 
-
   ##
-  # checks if the user can grant the api to organisations
+  # Can the User grant the api to organisations?
   #
-  # @return [Boolean] true if the user can grant api permissions to organisations
+  # Returns Boolean
   def can_grant_api_to_orgs?
     perms.include? Perm.grant_api
   end
 
-  ##
-  # removes the api_token from the user
-  # modifies the user model
+  # Removes the api_token from the user
+  #
+  # Returns nil
+  # Returns Boolean
   def remove_token!
     unless api_token.blank?
       update_column(:api_token, "") unless new_record?
     end
   end
 
-  ##
-  # generates a new token for the user unless the user already has a token.
-  # modifies the user's model.
+  # Generates a new token for the user unless the user already has a token.
+  #
+  # Returns nil
+  # Returns Boolean
   def keep_or_generate_token!
     if api_token.nil? || api_token.empty?
       self.api_token = loop do
@@ -305,10 +296,9 @@
     end
   end
 
-  ##
-  # Return the user's preferences for a given base key
+  # The User's preferences for a given base key
   #
-  # @return [JSON] with symbols as keys
+  # Returns Hash
   def get_preferences(key)
     defaults = Pref.default_settings[key.to_sym] || Pref.default_settings[key.to_s]
 
@@ -330,17 +320,19 @@
     end
   end
 
-  ##
   # Override devise_invitable email title
-  # --------------------------------------------------------------
   def deliver_invitation(options = {})
     super(options.merge(subject: _('A Data Management Plan in %{application_name} has been shared with you') % {application_name: Rails.configuration.branding[:application][:name]}))
   end
-  ##
+
   # Case insensitive search over User model
-  # @param field [string] The name of the field being queried
-  # @param val [string] The string to search for, case insensitive. val is duck typed to check whether or not downcase method exist
-  # @return [ActiveRecord::Relation] The result of the search
+  #
+  # field - The name of the field being queried
+  # val   - The String to search for, case insensitive. val is duck typed to check
+  #         whether or not downcase method exist.
+  #
+  # Returns ActiveRecord::Relation
+  # Raises ArgumentError
   def self.where_case_insensitive(field, val)
     unless columns.map(&:name).include?(field.to_s)
       raise ArgumentError, "Field #{field} is not present on users table"
@@ -348,8 +340,12 @@
     User.where("LOWER(#{field}) = :value", value: val.to_s.downcase)
   end
 
-  # Acknoledge a Notification
-  # @param notification Notification to acknowledge
+  # Acknowledge a Notification
+  #
+  # notification - Notification to acknowledge
+  #
+  # Returns ActiveRecord::Associations::CollectionProxy
+  # Returns nil
   def acknowledge(notification)
     notifications << notification if notification.dismissable?
   end
diff --git a/app/services/guidance_service.rb b/app/services/guidance_service.rb
index 0e773d7..947c4ed 100644
--- a/app/services/guidance_service.rb
+++ b/app/services/guidance_service.rb
@@ -6,6 +6,7 @@
     @plan = plan
     @guidance_groups = plan.guidance_groups.where(published: true)
   end
+
   # Returns an Array of orgs according to the guidance related to plan
   # Note the Array is sorted in the following order:
   # First funder org (if the template from the plan is a customization of another)
@@ -80,6 +81,36 @@
     return hashified_annotations[org].select{ |annotation| (annotation.question_id == question.id) && (annotation.type == "guidance")}
   end
 
+
+  # filters through the orgs with annotations and guidance groups to create a
+  # set of tabs with display names and any guidance/annotations to show
+  #
+  # question  - The question to which guidance pretains
+  #
+  # Returns an array of tab hashes.  These
+  def tablist(question)
+    # start with orgs
+    # filter into hash with annotation_presence, main_group presence, and
+    display_tabs = []
+    orgs.each do |org|
+      annotations = guidance_annotations(org: org,question: question)
+      groups = guidance_groups_by_theme(org: org,question: question)
+      main_groups = groups.select{|group| group.optional_subset == false}
+      subsets = groups.reject{|group| group.optional_subset == false}
+      if annotations.present? || main_groups.present? # annotations and main group
+        # Tab with org.abbreviation
+        display_tabs << {name: org.abbreviation, groups: main_groups,
+                        annotations: annotations}
+      end
+      if subsets.present?
+        subsets.each_pair do |group,theme|
+          display_tabs << {name: group.name.truncate(15), groups:{group => theme}}
+        end
+      end
+    end
+    return display_tabs
+  end
+
   private
     def orgs_from_guidance_groups
       if !defined?(@orgs_from_guidance_groups)
diff --git a/app/views/guidance_groups/_index_by_theme.html.erb b/app/views/guidance_groups/_index_by_theme.html.erb
index 9afb77e..3c39eff 100644
--- a/app/views/guidance_groups/_index_by_theme.html.erb
+++ b/app/views/guidance_groups/_index_by_theme.html.erb
@@ -20,7 +20,7 @@
           aria-controls="<%= "##{guidances.object_id}" %>">
           <div class="panel-heading" role="tab" id="<%= "panel-heading-#{guidances.object_id}" %>">
             <h2 class="panel-title">
-              <%= _("%{name} on %{title}") % { :name => guidance_group.name, :title => theme.title } %>
+              <%= theme.title %>
               <i class="fa fa-plus pull-right" aria-hidden="true"></i>
             </h2>
           </div>
diff --git a/app/views/org_admin/phases/_phase.html.erb b/app/views/org_admin/phases/_phase.html.erb
index 9f10f42..7571d4a 100644
--- a/app/views/org_admin/phases/_phase.html.erb
+++ b/app/views/org_admin/phases/_phase.html.erb
@@ -37,7 +37,7 @@
           </thead>
           <tbody>
             <% phase.sections.each do |section| %>
-              <tr>
+              <tr id="<%= dom_id(section) %>" data-number="<%= section.number %>">
                 <td><p><%= section.title %></p></td>
                 <td>
                   <% if section.questions.present? %>
diff --git a/app/views/phases/_guidances_notes.html.erb b/app/views/phases/_guidances_notes.html.erb
index 45d47de..1eb0959 100644
--- a/app/views/phases/_guidances_notes.html.erb
+++ b/app/views/phases/_guidances_notes.html.erb
@@ -23,54 +23,52 @@
   </ul>
   <div class="tab-content">
     <% if guidances_active %>
-    <div id="guidances-<%= question.id %>" role="tabpanel" class="tab-pane active">
-      <ul class="nav nav-tabs" role="tablist">
-        <% guidance_service.orgs.each_with_index do |org, i| %>
-            <% if guidance_service.any?(org: org, question: question) %>
-              <% active_nav ||= org.id %>
-              <li role="presentation" <%= active_nav == org.id ? "class=active" : "" %>>
-                <a
-                  data-target="<%= "#guidance_per_question_#{question.id}_#{i}" %>"
-                  aria-controls="<%= "#guidance_per_question_#{question.id}_#{i}" %>"
-                  role="tab"
-                  data-toggle="tab"
-                  class="view-plan-guidance">
-                  <%= org.abbreviation %>
-                </a>
-              </li>
-            <% end %>
-        <% end %>
-      </ul>
-      <div class="tab-content">
-        <% guidance_service.orgs.each_with_index do |org, i| %>
-          <% if guidance_service.any?(org: org, question: question) %>
-            <div id="<%= "guidance_per_question_#{question.id}_#{i}" %>" role="tabpanel" class="tab-pane <%= active_nav == org.id ? 'active' : '' %>">
-              <div class="panel panel-default">
-                <div class="panel-body">
-                  <% guidance_service.guidance_annotations(org: org, question: question).each do |annotation| %>
-                    <%=
-                      render partial: 'org_admin/annotations/show', locals: {
-                        template: template,
-                        example_answer: nil,
-                        guidance: annotation,
-                        for_plan: true }
-                    %>
-                  <% end %>
-                  <% if guidance_service.guidance_annotations?(org: org, question: question) &&
-                    guidance_service.guidance_groups_by_theme?(org: org, question: question) %>
-                    <hr />
-                  <% end %>
-                  <% if guidance_service.guidance_groups_by_theme?(org: org, question: question) %>
-                    <%= render partial: 'guidance_groups/index_by_theme',
-                        locals: { guidance_groups_by_theme: guidance_service.guidance_groups_by_theme(org: org, question: question) } %>
-                  <% end %>
+      <% tablist = guidance_service.tablist(question) %>
+      <div id="guidances-<%= question.id %>" role="tabpanel" class="tab-pane active">
+        <ul class="nav nav-tabs" role="tablist">
+          <% tablist.each_with_index do |tab, i| %>
+            <% active_nav ||= tab[:name] %>
+            <li role="presentation" <%= active_nav == tab[:name] ? "class=active" : "" %>>
+              <a
+                data-target="<%= "#guidance_per_question_#{question.id}_#{i}" %>"
+                aria-controls="<%= "#guidance_per_question_#{question.id}_#{i}" %>"
+                role="tab"
+                data-toggle="tab"
+                class="view-plan-guidance">
+                <%= tab[:name] %>
+              </a>
+            </li>
+          <% end %>
+        </ul>
+        <div class="tab-content">
+          <% tablist.each_with_index do |tab, i| %>
+            <div id="<%= "guidance_per_question_#{question.id}_#{i}" %>" role="tabpanel" class="tab-pane <%= active_nav == tab[:name] ? 'active' : '' %>">
+                <div class="panel panel-default">
+                  <div class="panel-body">
+                    <% if tab[:annotations].present? %>
+                      <% tab[:annotations].each do |annotation| %>
+                        <%=
+                          render partial: 'org_admin/annotations/show', locals: {
+                            template: template,
+                            example_answer: nil,
+                            guidance: annotation,
+                            for_plan: true }
+                        %>
+                      <% end %>
+                      <% if tab[:groups].present? %>
+                        <hr />
+                      <% end %>
+                    <% end %>
+                    <% if tab[:groups].present? %>
+                      <%= render partial: 'guidance_groups/index_by_theme',
+                          locals: { guidance_groups_by_theme: tab[:groups] } %>
+                    <% end %>
+                  </div>
                 </div>
               </div>
-            </div>
           <% end %>
-        <% end %>
+        </div>
       </div>
-    </div>
     <% end %>
 
     <% if plan.present? %>
diff --git a/app/views/shared/_create_account_form.html.erb b/app/views/shared/_create_account_form.html.erb
index 6bdf261..3ed5abe 100644
--- a/app/views/shared/_create_account_form.html.erb
+++ b/app/views/shared/_create_account_form.html.erb
@@ -15,7 +15,7 @@
   <div class="form-group">
     <%= render partial: "shared/my_org",
                locals: {f: f, default_org: @default_org,
-                        orgs: Org.where("parent_id IS NULL").order("sort_name ASC, name ASC"),
+                        orgs: Org.order("sort_name ASC, name ASC"),
                         allow_other_orgs: true, required: true} %>
   </div>
 
diff --git a/app/views/shared/export/_plan.erb b/app/views/shared/export/_plan.erb
index d6db153..b830166 100644
--- a/app/views/shared/export/_plan.erb
+++ b/app/views/shared/export/_plan.erb
@@ -32,55 +32,57 @@
     <% end %>
 
     <% @hash[:phases].each do |phase| %>
-      <div style="page-break-before:always;"></div> <!-- Page break before each phase -->
-      <!-- If there is more than one phase show the plan title and phase title -->
-      <h1><%= (@hash[:phases].length > 1 ? "#{@plan.title} - #{phase[:title]}" : @plan.title) %></h1>
-      <hr />
-      <% phase[:sections].each do |section| %>
-        <% if @show_sections_questions %>
-          <h3><%= section[:title] %></h3>
-        <% end %>
+      <%# Only render selected phase %>
+      <% if phase[:title] == @selected_phase.title %>
+        <div style="page-break-before:always;"></div> <!-- Page break before each phase -->
+        <h1><%= download_plan_page_title(@plan, phase, @hash) %></h1>
+        <hr />
+        <% phase[:sections].each do |section| %>
+          <% if display_questions_and_section_headings(section, @show_sections_questions, @show_custom_sections) %>
+            <h3><%= section[:title] %></h3>
 
-        <% section[:questions].each do |question| %>
-          <div class="question">
-            <% if @show_sections_questions && !@public_plan %>
-              <p><%= raw question[:text].gsub(/<tr>(\s|<td>|<\/td>|&nbsp;)*(<\/tr>|<tr>)/,"") if question[:text].present?%></p>
-              <br>
-            <% end %>
-            <% answer = @plan.answer(question[:id], false) %>
-            <% blank = answer.present? ? answer.is_blank? : true %>
-            <% options = answer.present? ? answer.question_options : [] %>
-            <%# case where question has not been answered sufficiently to display%>
-            <% if @show_unanswered && (answer.blank? || (options.blank? && blank))%>
-              <p><%= _('Question not answered.') -%></p>
-            <% else %>
-              <%# case where Question has options %>
-              <% if options.present?%>
-                <ul>
-                  <% options.each do |opt| %>
-                    <li><%= opt.text %></li>
-                  <% end %>
-                </ul>
-              <% end %>
-              <%# case for RDA answer display %>
-              <% if question[:format].rda_metadata? && !blank %>
-                <% ah = answer.answer_hash %>
-                <% if ah['standards'].present? %>
-                  <ul>
-                    <% ah['standards'].each do |id, title| %>
-                      <li><%= title %></li>
-                    <% end %>
-                  </ul>
+            <% section[:questions].each do |question| %>
+              <div class="question">
+                <% if !@public_plan %>
+                  <p><%= raw question[:text].gsub(/<tr>(\s|<td>|<\/td>|&nbsp;)*(<\/tr>|<tr>)/,"") if question[:text].present?%></p>
+                  <br>
                 <% end %>
-                <p><%= raw ah['text'] %></p>
-              <%# case for displaying comments OR text %>
-              <% elsif !blank %>
-                <p><%= raw answer.text %></p>
-              <% end %>
+                <% answer = @plan.answer(question[:id], false) %>
+                <% blank = answer.present? ? answer.is_blank? : true %>
+                <% options = answer.present? ? answer.question_options : [] %>
+                <%# case where question has not been answered sufficiently to display%>
+                <% if @show_unanswered && (answer.blank? || (options.blank? && blank))%>
+                  <p><%= _('Question not answered.') -%></p>
+                <% else %>
+                  <%# case where Question has options %>
+                  <% if options.any? %>
+                    <ul>
+                      <% options.each do |opt| %>
+                        <li><%= opt.text %></li>
+                      <% end %>
+                    </ul>
+                  <% end %>
+                  <%# case for RDA answer display %>
+                  <% if question[:format].rda_metadata? && !blank %>
+                    <% ah = answer.answer_hash %>
+                    <% if ah['standards'].present? %>
+                      <ul>
+                        <% ah['standards'].each do |id, title| %>
+                          <li><%= title %></li>
+                        <% end %>
+                      </ul>
+                    <% end %>
+                    <p><%= raw ah['text'] %></p>
+                  <%# case for displaying comments OR text %>
+                  <% elsif !blank %>
+                    <p><%= raw answer.text %></p>
+                  <% end %>
+                <% end %>
+              </div>
             <% end %>
-          </div>
-        <% end %>
-      <% end %> <!-- sections.each -->
+          <% end %>
+        <% end %> <!-- sections.each -->
+      <% end %>
     <% end %>
   </body>
 </html>
diff --git a/app/views/shared/export/_plan_txt.erb b/app/views/shared/export/_plan_txt.erb
index 6b06132..d2be1c2 100644
--- a/app/views/shared/export/_plan_txt.erb
+++ b/app/views/shared/export/_plan_txt.erb
@@ -22,13 +22,14 @@
 <% end %>
 
 <% @hash[:phases].each do |phase| %>
-<%= (@hash[:phases].length > 1 ? "#{phase[:title]}" : "") %>
+<%# Only render selected phase %>
+<% if phase[:title] == @selected_phase.title %>
+  <%= (@hash[:phases].length > 1 ? "#{phase[:title]}" : "") %>
   <% phase[:sections].each do |section| %>
-    <% if @show_sections_questions %>
+    <% if display_questions_and_section_headings(section, @show_sections_questions, @show_custom_sections) %>
 <%= "#{section[:title]}\n" %>
-    <% end %>
-    <% section[:questions].each do |question| %>
-      <% if @show_sections_questions %>
+
+      <% section[:questions].each do |question| %>
         <%# text in this case is an array to accomodate for option_based %>
         <% if question[:text].respond_to?(:each) %>
           <% question[:text].each do |txt| %>
@@ -37,22 +38,22 @@
         <% else %>
 <%= "#{strip_tags(question[:text][0].gsub(/<tr>(\s|<td>|<\/td>|&nbsp;)*(<\/tr>|<tr>)/,""))}\n" if question[:text].present? && question[:text][0].present? %>
         <% end %>
-      <% end %>
-      <% answer = @plan.answer(question[:id], false) %>
-      <% blank = (answer.present? && answer.is_valid?) ? answer.text.gsub(/<\/?p>/, '').gsub(/<br\s?\/?>/, '\n').chomp.blank? : true %>
-      <% if blank && @show_unanswered %>
+        <% answer = @plan.answer(question[:id], false) %>
+        <% blank = (answer.present? && answer.is_valid?) ? answer.text.gsub(/<\/?p>/, '').gsub(/<br\s?\/?>/, '\n').chomp.blank? : true %>
+        <% if blank && @show_unanswered %>
 <%= "    #{_("Question not answered.")}\n\n" %>
-      <% elsif !blank %>
-        <% if answer.question_options.length > 0 %>
-          <% answer.question_options.each do |opt| %>
+        <% elsif !blank %>
+          <% if answer.question_options.length > 0 %>
+            <% answer.question_options.each do |opt| %>
 <%= "    #{opt.text}\n" %>
+            <% end %>
+          <% end %>
+<%= "    #{strip_tags(answer.text.gsub(/<\/?p>/, '').gsub(/<br\s?\/?>/, '\n').chomp)}\n\n" if answer.text.present? %>
           <% end %>
         <% end %>
-<%= "    #{strip_tags(answer.text.gsub(/<\/?p>/, '').gsub(/<br\s?\/?>/, '\n').chomp)}\n\n" if answer.text.present? %>
       <% end %>
     <% end %>
   <% end %>
 <% end %>
-
 <%= "----------------------------------------------------------" %>
 <%= _("A Data Management Plan created using %{application_name}") % { application_name: Rails.configuration.branding[:application][:name] } %>
\ No newline at end of file
diff --git a/bin/rubocop_changed b/bin/rubocop_changed
new file mode 100755
index 0000000..08c8e49
--- /dev/null
+++ b/bin/rubocop_changed
@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+
+# Which branch should we compare HEAD with for changed files? (defaults: 'development')
+BRANCH='development'
+DIRS='app lib'
+
+while getopts 'b:d:' optname
+do
+  case "$optname" in
+    "b")
+      BRANCH=$OPTARG
+      ;;
+    "d")
+      DIRS=$OPTARG
+      ;;
+  esac
+done
+
+# Get a list of all files that have changed on this branch in app and lib directories.
+CHANGED_FILES=$(git diff --name-only $BRANCH -- $DIRS)
+
+# A string with the name of each changed file
+EXISTING_FILES=""
+
+# Iterate over each changed file
+for FILEPATH in $CHANGED_FILES
+do
+  # Append this filename if the file still exists (in case the file has been deleted)
+  if [ -f $FILEPATH ]; then
+    EXISTING_FILES+=" $FILEPATH"
+  fi
+done
+
+# If there are no files that have been changed...
+if [ -z "$EXISTING_FILES" ]
+then
+  # Print a message and exit
+  echo "Rubocop changed: No matching files have changed."
+  exit 0
+else
+  # Run Rubocop against the files that have chagned
+  rubocop -p $EXISTING_FILES
+fi
diff --git a/db/migrate/20130905073232_remove_slug_from_plans.rb b/db/migrate/20130905073232_remove_slug_from_plans.rb
deleted file mode 100644
index a06bdee..0000000
--- a/db/migrate/20130905073232_remove_slug_from_plans.rb
+++ /dev/null
@@ -1,9 +0,0 @@
-class RemoveSlugFromPlans < ActiveRecord::Migration
-  def up
-  	remove_column :plans, :slug
-  end
-
-  def down
-  	add_column :plans, :slug, :string
-  end
-end
diff --git a/db/migrate/20170303220255_remove_orcid_id_from_users.rb b/db/migrate/20170303220255_remove_orcid_id_from_users.rb
deleted file mode 100644
index 7c71213..0000000
--- a/db/migrate/20170303220255_remove_orcid_id_from_users.rb
+++ /dev/null
@@ -1,5 +0,0 @@
-class RemoveOrcidIdFromUsers < ActiveRecord::Migration
-  def change
-    #remove_column :users, :orcid_id
-  end
-end
diff --git a/db/migrate/20180813114157_remove_logo_file_name_from_orgs.rb b/db/migrate/20180813114157_remove_logo_file_name_from_orgs.rb
new file mode 100644
index 0000000..334fdd7
--- /dev/null
+++ b/db/migrate/20180813114157_remove_logo_file_name_from_orgs.rb
@@ -0,0 +1,11 @@
+class RemoveLogoFileNameFromOrgs < ActiveRecord::Migration
+  def up
+    if column_exists?(:orgs, :logo_file_name)
+      remove_column :orgs, :logo_file_name
+    end
+  end
+
+  def down
+    add_column :orgs, :logo_file_name, :string
+  end
+end
diff --git a/db/migrate/20180813114216_remove_parent_id_from_orgs.rb b/db/migrate/20180813114216_remove_parent_id_from_orgs.rb
new file mode 100644
index 0000000..118125b
--- /dev/null
+++ b/db/migrate/20180813114216_remove_parent_id_from_orgs.rb
@@ -0,0 +1,11 @@
+class RemoveParentIdFromOrgs < ActiveRecord::Migration
+  def up
+    if column_exists?(:orgs, :parent_id)
+      remove_column :orgs, :parent_id
+    end
+  end
+
+  def down
+    add_column :orgs, :parent_id, :integer
+  end
+end
diff --git a/db/migrate/20180813114234_remove_wayfless_entity_from_orgs.rb b/db/migrate/20180813114234_remove_wayfless_entity_from_orgs.rb
new file mode 100644
index 0000000..a19bb0c
--- /dev/null
+++ b/db/migrate/20180813114234_remove_wayfless_entity_from_orgs.rb
@@ -0,0 +1,11 @@
+class RemoveWayflessEntityFromOrgs < ActiveRecord::Migration
+  def up
+    if column_exists?(:orgs, :wayfless_entity)
+      remove_column :orgs, :wayfless_entity
+    end
+  end
+
+  def down
+    add_column :orgs, :wayfless_entity, :string
+  end
+end
diff --git a/db/migrate/20180813114348_remove_slug_from_phases.rb b/db/migrate/20180813114348_remove_slug_from_phases.rb
new file mode 100644
index 0000000..3520ef6
--- /dev/null
+++ b/db/migrate/20180813114348_remove_slug_from_phases.rb
@@ -0,0 +1,11 @@
+class RemoveSlugFromPhases < ActiveRecord::Migration
+  def up
+    if column_exists?(:phases, :slug)
+      remove_column :phases, :slug
+    end
+  end
+
+  def down
+    add_column :phases, :slug, :string
+  end
+end
diff --git a/db/migrate/20180813114525_remove_slug_from_plans.rb b/db/migrate/20180813114525_remove_slug_from_plans.rb
new file mode 100644
index 0000000..11ebb04
--- /dev/null
+++ b/db/migrate/20180813114525_remove_slug_from_plans.rb
@@ -0,0 +1,11 @@
+class RemoveSlugFromPlans < ActiveRecord::Migration
+  def up
+    if column_exists?(:plans, :slug)
+      remove_column :plans, :slug
+    end
+  end
+
+  def down
+    add_column :plans, :slug, :string
+  end
+end
diff --git a/db/migrate/20180813114550_drop_table_friendly_id_slugs.rb b/db/migrate/20180813114550_drop_table_friendly_id_slugs.rb
new file mode 100644
index 0000000..8d0ab2e
--- /dev/null
+++ b/db/migrate/20180813114550_drop_table_friendly_id_slugs.rb
@@ -0,0 +1,17 @@
+class DropTableFriendlyIdSlugs < ActiveRecord::Migration
+  def up
+    drop_table :friendly_id_slugs if table_exists?(:friendly_id_slugs)
+  end
+
+  def down
+    create_table :friendly_id_slugs do |t|
+      t.string   :slug,           :null => false
+      t.integer  :sluggable_id,   :null => false
+      t.string   :sluggable_type, :limit => 40
+      t.datetime :created_at
+    end
+    add_index :friendly_id_slugs, :sluggable_id
+    add_index :friendly_id_slugs, [:slug, :sluggable_type], :unique => true
+    add_index :friendly_id_slugs, :sluggable_type
+  end
+end
diff --git a/db/migrate/20180813114614_drop_table_file_types.rb b/db/migrate/20180813114614_drop_table_file_types.rb
new file mode 100644
index 0000000..d0be6f1
--- /dev/null
+++ b/db/migrate/20180813114614_drop_table_file_types.rb
@@ -0,0 +1,17 @@
+class DropTableFileTypes < ActiveRecord::Migration
+
+  def up
+    drop_table(:file_types) if table_exists?(:file_types)
+  end
+
+  def down
+    create_table "file_types", force: :cascade do |t|
+      t.string   "name"
+      t.string   "icon_name"
+      t.integer  "icon_size"
+      t.string   "icon_location"
+      t.datetime "created_at",    null: false
+      t.datetime "updated_at",    null: false
+    end
+  end
+end
diff --git a/db/migrate/20180813114622_drop_table_file_uploads.rb b/db/migrate/20180813114622_drop_table_file_uploads.rb
new file mode 100644
index 0000000..efc1f5c
--- /dev/null
+++ b/db/migrate/20180813114622_drop_table_file_uploads.rb
@@ -0,0 +1,19 @@
+class DropTableFileUploads < ActiveRecord::Migration
+  def up
+    drop_table(:file_uploads) if table_exists?(:file_uploads)
+  end
+
+  def down
+    create_table "file_uploads", force: :cascade do |t|
+      t.string   "name"
+      t.string   "title"
+      t.text     "description"
+      t.integer  "size"
+      t.boolean  "published"
+      t.string   "location"
+      t.integer  "file_type_id"
+      t.datetime "created_at",   null: false
+      t.datetime "updated_at",   null: false
+    end
+  end
+end
diff --git a/db/migrate/20180813114628_drop_table_splash_logs.rb b/db/migrate/20180813114628_drop_table_splash_logs.rb
new file mode 100644
index 0000000..b09cc0b
--- /dev/null
+++ b/db/migrate/20180813114628_drop_table_splash_logs.rb
@@ -0,0 +1,13 @@
+class DropTableSplashLogs < ActiveRecord::Migration
+  def up
+    drop_table(:splash_logs) if table_exists?(:splash_logs)
+  end
+
+  def down
+    create_table "splash_logs", force: :cascade do |t|
+      t.string   "destination"
+      t.datetime "created_at",  null: false
+      t.datetime "updated_at",  null: false
+    end
+  end
+end
diff --git a/db/migrate/20180813114649_remove_banner_text_from_orgs.rb b/db/migrate/20180813114649_remove_banner_text_from_orgs.rb
new file mode 100644
index 0000000..315e4b4
--- /dev/null
+++ b/db/migrate/20180813114649_remove_banner_text_from_orgs.rb
@@ -0,0 +1,9 @@
+class RemoveBannerTextFromOrgs < ActiveRecord::Migration
+  def up
+    remove_column :orgs, :banner_text
+  end
+
+  def down
+    add_column :orgs, :banner_text, :text
+  end
+end
diff --git a/db/migrate/20180813114719_remove_question_id_from_guidances.rb b/db/migrate/20180813114719_remove_question_id_from_guidances.rb
new file mode 100644
index 0000000..4849d84
--- /dev/null
+++ b/db/migrate/20180813114719_remove_question_id_from_guidances.rb
@@ -0,0 +1,9 @@
+class RemoveQuestionIdFromGuidances < ActiveRecord::Migration
+  def up
+    remove_column :guidances, :question_id
+  end
+
+  def down
+    add_column :guidances, :question_id, :integer
+  end
+end
diff --git a/db/migrate/20180813114801_remove_orcid_id_from_users.rb b/db/migrate/20180813114801_remove_orcid_id_from_users.rb
new file mode 100644
index 0000000..aa89421
--- /dev/null
+++ b/db/migrate/20180813114801_remove_orcid_id_from_users.rb
@@ -0,0 +1,9 @@
+class RemoveOrcidIdFromUsers < ActiveRecord::Migration
+  def up
+    remove_column :users, :orcid_id
+  end
+
+  def down
+    add_column :users, :orcid_id, :string
+  end
+end
diff --git a/db/migrate/20180813114813_remove_shibboleth_id_from_users.rb b/db/migrate/20180813114813_remove_shibboleth_id_from_users.rb
new file mode 100644
index 0000000..51cd451
--- /dev/null
+++ b/db/migrate/20180813114813_remove_shibboleth_id_from_users.rb
@@ -0,0 +1,9 @@
+class RemoveShibbolethIdFromUsers < ActiveRecord::Migration
+  def up
+    remove_column :users, :shibboleth_id
+  end
+
+  def down
+    add_column :users, :shibboleth_id, :string
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 422ac3c..41ee2bf 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20180807121126) do
+ActiveRecord::Schema.define(version: 20180813114813) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -56,27 +56,6 @@
     t.integer  "phase_id"
   end
 
-  create_table "file_types", force: :cascade do |t|
-    t.string   "name"
-    t.string   "icon_name"
-    t.integer  "icon_size"
-    t.string   "icon_location"
-    t.datetime "created_at",    null: false
-    t.datetime "updated_at",    null: false
-  end
-
-  create_table "file_uploads", force: :cascade do |t|
-    t.string   "name"
-    t.string   "title"
-    t.text     "description"
-    t.integer  "size"
-    t.boolean  "published"
-    t.string   "location"
-    t.integer  "file_type_id"
-    t.datetime "created_at",   null: false
-    t.datetime "updated_at",   null: false
-  end
-
   create_table "guidance_groups", force: :cascade do |t|
     t.string   "name"
     t.integer  "org_id"
@@ -93,7 +72,6 @@
     t.integer  "guidance_group_id"
     t.datetime "created_at",        null: false
     t.datetime "updated_at",        null: false
-    t.integer  "question_id"
     t.boolean  "published"
   end
 
@@ -172,14 +150,10 @@
     t.string   "name"
     t.string   "abbreviation"
     t.string   "target_url"
-    t.string   "wayfless_entity"
     t.datetime "created_at",                             null: false
     t.datetime "updated_at",                             null: false
-    t.integer  "parent_id"
     t.boolean  "is_other",               default: false, null: false
     t.string   "sort_name"
-    t.text     "banner_text"
-    t.string   "logo_file_name"
     t.integer  "region_id"
     t.integer  "language_id"
     t.string   "logo_uid"
@@ -206,7 +180,6 @@
     t.integer  "template_id"
     t.datetime "created_at"
     t.datetime "updated_at"
-    t.string   "slug"
     t.boolean  "modifiable"
   end
 
@@ -217,7 +190,6 @@
     t.integer  "template_id"
     t.datetime "created_at"
     t.datetime "updated_at"
-    t.string   "slug"
     t.string   "grant_number"
     t.string   "identifier"
     t.text     "description"
@@ -329,12 +301,6 @@
     t.datetime "updated_at",  null: false
   end
 
-  create_table "splash_logs", force: :cascade do |t|
-    t.string   "destination"
-    t.datetime "created_at",  null: false
-    t.datetime "updated_at",  null: false
-  end
-
   create_table "templates", force: :cascade do |t|
     t.string   "title"
     t.text     "description"
@@ -395,8 +361,6 @@
     t.string   "firstname"
     t.string   "surname"
     t.string   "email",                  limit: 80, default: "",   null: false
-    t.string   "orcid_id"
-    t.string   "shibboleth_id"
     t.datetime "created_at",                                       null: false
     t.datetime "updated_at",                                       null: false
     t.string   "encrypted_password",                default: ""
diff --git a/lib/branding.rb b/lib/branding.rb
index 9427e98..2400d5c 100644
--- a/lib/branding.rb
+++ b/lib/branding.rb
@@ -5,15 +5,18 @@
 
   # Loads branding config from YAML file.
   #
-  # @param keys [Array<Object>] A list of the keys to return configs for.
+  # keys - A list of the keys to return configs for.
   #
-  # @example Return a value
+  # Examples:
+  #
+  #   # Return a value
   #   Branding.fetch(:settings, :should_work) # => true
   #   Branding.fetch(:settings, :email) # => 'user@example.com'
   #   Branding.fetch(:settings, :missing) # => nil
-  # @return [Object] The value of the config
+  #
+  # Returns Object
   def fetch(*keys)
     keys = keys.map(&:to_sym)
     Rails.configuration.branding.dig(*keys)
   end
-end
\ No newline at end of file
+end
diff --git a/lib/global_helpers.rb b/lib/global_helpers.rb
index b630113..8a01937 100644
--- a/lib/global_helpers.rb
+++ b/lib/global_helpers.rb
@@ -1,14 +1,17 @@
 module GlobalHelpers
 
   ##
-  # takes in a string which is meant to be constant, and looks it up in the default
-  # (en_GB) locale.  This should ensure that the back-end remains constant and consistantly called
+  # Takes in a string which is meant to be constant, and looks it up in the default
+  # (en_GB) locale.  This should ensure that the back-end remains constant and
+  # consistantly called
   #
-  # @param [String] str the string which will be looked up in the localisation
-  # @return [String] the constant which the string defines
+  # str - The String which will be looked up in the localisation
+  #
+  # Returns String
   def constant(str)
     I18n.t("magic_strings.#{str}", locale: I18n.default_locale)
   end
+
   # overloading the method
   # came across a wierd issue where the function would refused to be called from
   # class functions of other classes... but it will work if this is a class function
diff --git a/lib/tasks/doc.rake b/lib/tasks/doc.rake
new file mode 100644
index 0000000..96a0c4f
--- /dev/null
+++ b/lib/tasks/doc.rake
@@ -0,0 +1,38 @@
+namespace :tomdoc do
+  desc "Removes the docs from the ./doc directory"
+  task :clear  do
+    FileUtils.rm_r(Rails.root.join("doc"))
+  end
+
+  desc "Builds documentation in the ./doc directory"
+  task :app do
+    puts "Please wait..."
+    options = []
+    # Parse documentation as Tomdoc (https://tomdoc.org)
+    options << "--plugin tomdoc"
+    # Specify which file to use for the main index (README)
+    options << "--readme README.md"
+    # Hides return types specified as 'void'.
+    options << "--hide-void-return"
+    # Add a custom title to the HTML docs
+    options << "--title 'DMP Roadmap'"
+    # Include protected methods
+    options << "--protected"
+    # Include private methods
+    options << "--private"
+    # Set methods with no Return value to 'void'
+    options << "--default-return 'void'"
+    system("yard doc #{options.join(" ")}")
+  end
+
+  desc "Builds documentation in the ./doc directory"
+  task :open do
+    `open doc/index.html`
+  end
+end
+
+task tomdoc: ["tomdoc:clear", "tomdoc:app", "tomdoc:open"] do
+end
+
+# Clear Rails' default doc tasks first.
+task("doc:app").clear.enhance(["tomdoc:app"])
diff --git a/spec/factories/exported_plans.rb b/spec/factories/exported_plans.rb
index 110e7ae..d1a1c22 100644
--- a/spec/factories/exported_plans.rb
+++ b/spec/factories/exported_plans.rb
@@ -3,12 +3,12 @@
 # Table name: exported_plans
 #
 #  id         :integer          not null, primary key
-#  plan_id    :integer
-#  user_id    :integer
 #  format     :string
 #  created_at :datetime         not null
 #  updated_at :datetime         not null
 #  phase_id   :integer
+#  plan_id    :integer
+#  user_id    :integer
 #
 
 FactoryBot.define do
diff --git a/spec/factories/guidances.rb b/spec/factories/guidances.rb
index d57c1a0..43a8e68 100644
--- a/spec/factories/guidances.rb
+++ b/spec/factories/guidances.rb
@@ -8,7 +8,6 @@
 #  created_at        :datetime         not null
 #  updated_at        :datetime         not null
 #  guidance_group_id :integer
-#  question_id       :integer
 #
 # Indexes
 #
diff --git a/spec/factories/identifier_schemes.rb b/spec/factories/identifier_schemes.rb
index 03459e4..2f3deb9 100644
--- a/spec/factories/identifier_schemes.rb
+++ b/spec/factories/identifier_schemes.rb
@@ -3,13 +3,13 @@
 # Table name: identifier_schemes
 #
 #  id               :integer          not null, primary key
-#  name             :string
-#  description      :string
 #  active           :boolean
+#  description      :string
+#  logo_url         :text
+#  name             :string
+#  user_landing_url :text
 #  created_at       :datetime
 #  updated_at       :datetime
-#  logo_url         :text
-#  user_landing_url :text
 #
 
 FactoryBot.define do
diff --git a/spec/factories/languages.rb b/spec/factories/languages.rb
index 2350723..70af9db 100644
--- a/spec/factories/languages.rb
+++ b/spec/factories/languages.rb
@@ -4,9 +4,9 @@
 #
 #  id               :integer          not null, primary key
 #  abbreviation     :string
+#  default_language :boolean
 #  description      :string
 #  name             :string
-#  default_language :boolean
 #
 
 FactoryBot.define do
diff --git a/spec/factories/notifications.rb b/spec/factories/notifications.rb
index 3b5cac6..fd60bc7 100644
--- a/spec/factories/notifications.rb
+++ b/spec/factories/notifications.rb
@@ -3,13 +3,13 @@
 # Table name: notifications
 #
 #  id                :integer          not null, primary key
-#  notification_type :integer
-#  title             :string
-#  level             :integer
 #  body              :text
 #  dismissable       :boolean
-#  starts_at         :date
 #  expires_at        :date
+#  level             :integer
+#  notification_type :integer
+#  starts_at         :date
+#  title             :string
 #  created_at        :datetime         not null
 #  updated_at        :datetime         not null
 #
diff --git a/spec/factories/orgs.rb b/spec/factories/orgs.rb
index 2945f18..3d19e1b 100644
--- a/spec/factories/orgs.rb
+++ b/spec/factories/orgs.rb
@@ -4,7 +4,6 @@
 #
 #  id                     :integer          not null, primary key
 #  abbreviation           :string
-#  banner_text            :text
 #  contact_email          :string
 #  contact_name           :string
 #  feedback_email_msg     :text
@@ -12,18 +11,15 @@
 #  feedback_enabled       :boolean          default(FALSE)
 #  is_other               :boolean          default(FALSE), not null
 #  links                  :text
-#  logo_file_name         :string
 #  logo_name              :string
 #  logo_uid               :string
 #  name                   :string
 #  org_type               :integer          default(0), not null
 #  sort_name              :string
 #  target_url             :string
-#  wayfless_entity        :string
 #  created_at             :datetime         not null
 #  updated_at             :datetime         not null
 #  language_id            :integer
-#  parent_id              :integer
 #  region_id              :integer
 #
 # Foreign Keys
diff --git a/spec/factories/phases.rb b/spec/factories/phases.rb
index 9cb7d85..c51c4f2 100644
--- a/spec/factories/phases.rb
+++ b/spec/factories/phases.rb
@@ -6,7 +6,6 @@
 #  description :text
 #  modifiable  :boolean
 #  number      :integer
-#  slug        :string
 #  title       :string
 #  created_at  :datetime
 #  updated_at  :datetime
diff --git a/spec/factories/plans.rb b/spec/factories/plans.rb
index bbb922b..c91a105 100644
--- a/spec/factories/plans.rb
+++ b/spec/factories/plans.rb
@@ -16,7 +16,6 @@
 #  principal_investigator_email      :string
 #  principal_investigator_identifier :string
 #  principal_investigator_phone      :string
-#  slug                              :string
 #  title                             :string
 #  visibility                        :integer          default(3), not null
 #  created_at                        :datetime
diff --git a/spec/factories/question_formats.rb b/spec/factories/question_formats.rb
index 3e84c1a..335fe64 100644
--- a/spec/factories/question_formats.rb
+++ b/spec/factories/question_formats.rb
@@ -3,12 +3,12 @@
 # Table name: question_formats
 #
 #  id           :integer          not null, primary key
-#  title        :string
 #  description  :text
+#  formattype   :integer          default(0)
+#  option_based :boolean          default(FALSE)
+#  title        :string
 #  created_at   :datetime         not null
 #  updated_at   :datetime         not null
-#  option_based :boolean          default(FALSE)
-#  formattype   :integer          default(0)
 #
 
 FactoryBot.define do
diff --git a/spec/factories/themes.rb b/spec/factories/themes.rb
index 9dc836d..bd117b0 100644
--- a/spec/factories/themes.rb
+++ b/spec/factories/themes.rb
@@ -3,11 +3,11 @@
 # Table name: themes
 #
 #  id          :integer          not null, primary key
-#  title       :string
 #  description :text
+#  locale      :string
+#  title       :string
 #  created_at  :datetime         not null
 #  updated_at  :datetime         not null
-#  locale      :string
 #
 
 FactoryBot.define do
diff --git a/spec/factories/token_permission_types.rb b/spec/factories/token_permission_types.rb
index bcccca1..4677cdf 100644
--- a/spec/factories/token_permission_types.rb
+++ b/spec/factories/token_permission_types.rb
@@ -3,8 +3,8 @@
 # Table name: token_permission_types
 #
 #  id               :integer          not null, primary key
-#  token_type       :string
 #  text_description :text
+#  token_type       :string
 #  created_at       :datetime
 #  updated_at       :datetime
 #
diff --git a/spec/factories/users.rb b/spec/factories/users.rb
index 0f32562..d6cf3dd 100644
--- a/spec/factories/users.rb
+++ b/spec/factories/users.rb
@@ -32,9 +32,7 @@
 #  updated_at             :datetime         not null
 #  invited_by_id          :integer
 #  language_id            :integer
-#  orcid_id               :string
 #  org_id                 :integer
-#  shibboleth_id          :string
 #
 # Indexes
 #