diff --git a/app/admin/org.rb b/app/admin/org.rb
new file mode 100644
index 0000000..0f92a58
--- /dev/null
+++ b/app/admin/org.rb
@@ -0,0 +1,110 @@
+# [+Project:+] DMPRoadmap
+# [+Description:+]
+#
+# [+Created:+] 03/09/2014
+# [+Copyright:+] Digital Curation Centre and University of California Curation Center
+
+ActiveAdmin.register Org do
+	permit_params :abbreviation, :banner_file_id, :description, :logo_file_id, :name, :target_url, :organisation_type_id, :wayfless_entity, :parent_id
+
+	 menu :priority => 14, :label => proc{I18n.t('admin.org')}, :parent => "Organisations management"
+
+	index do
+        column I18n.t('admin.org_title'), :sortable => :name do |ggn|
+            link_to ggn.name, [:admin, ggn]
+        end
+        column I18n.t('admin.abbrev'), :sortable => :abbreviation do |ggn|
+            if !ggn.abbreviation.nil?
+                link_to ggn.abbreviation, [:admin, ggn]
+            else
+                '-'
+            end
+        end
+        column I18n.t('admin.org_type'), :sortable => :organisation_type_id do |org_type|
+            if !org_type.organisation_type_id.nil? then
+                link_to org_type.organisation_type.name, [:admin, org_type]
+            end
+        end
+
+         actions
+    end
+
+
+    #show details of an organisation
+    show do
+        resource.check_api_credentials
+		attributes_table do
+			row I18n.t('admin.org_title'), :sortable => :name do |gn|
+				if !gn.name.nil? then
+                    link_to gn.name, [:admin, gn]
+                end
+            end
+			row I18n.t('admin.abbrev'), :abbreviation do |ggn|
+                if !ggn.abbreviation.nil?
+                    link_to ggn.abbreviation, [:admin, ggn]
+                else
+                    '-'
+                end
+			end
+			row :sort_name
+			row I18n.t('admin.org_type'), :organisation_type_id do |org_type|
+				if !org_type.organisation_type_id.nil? then
+                    link_to org_type.organisation_type.name, [:admin, org_type]
+                end
+            end
+            row :banner_text do |banner|
+                if !banner.banner_text.nil? then
+                    banner.banner_text.html_safe
+                end
+            end
+        #    row :target_url
+            row :logo_file_name
+            row :wayfless_entity
+            row I18n.t('admin.token_permission_type') do
+                (organisation.token_permission_types.map{|tpt| link_to tpt.token_type, [:admin, tpt]}).join(', ').html_safe
+            end
+            row :created_at
+            row :updated_at
+		end
+	end
+
+	#templates sidebar
+ 	sidebar I18n.t('admin.templates'), :only => :show, :if => proc { organisation.dmptemplates.count >= 1} do
+	 	table_for organisation.dmptemplates.order("title asc") do |temp|
+	 		column :title do |dmptemp|
+                link_to dmptemp.title, [:admin, dmptemp]
+            end
+            column :published
+	 	end
+	end
+
+	#form
+    form do |f|
+        f.inputs "Details" do
+            f.input :name
+            f.input :abbreviation
+            f.input :sort_name
+            f.input :organisation_type_id, :label => I18n.t('admin.org_type'), :as => :select, :collection => OrganisationType.order('name').map{|orgt|[orgt.name, orgt.id]}
+        #    f.input :target_url
+            f.input :banner_text
+            f.input :logo_file_name
+            f.input :wayfless_entity
+            f.input :token_permission_types, label: I18n.t('admin.token_permission_type'),
+                    as: :select, multiple: true, include_blank: I18n.t('helpers.none'),
+                    collection: TokenPermissionType.order(:token_type).map{|token| [token.token_type, token.id]},
+                    hint: I18n.t('admin.choose_api_permissions')
+        #    f.input :parent_id, :label => I18n.t('admin.org_parent'), :as => :select, :collection => Organisation.find(:all, :order => 'name ASC').map{|orgp|[orgp.name, orgp.id]}
+        #    f.input :stylesheet_file_id
+        end
+        f.actions
+    end
+
+
+	 controller do
+		def permitted_params
+		  params.permit!
+		end
+  end
+
+
+end
diff --git a/app/admin/organisation.rb b/app/admin/organisation.rb
deleted file mode 100644
index 2357eb3..0000000
--- a/app/admin/organisation.rb
+++ /dev/null
@@ -1,110 +0,0 @@
-# [+Project:+] DMPRoadmap
-# [+Description:+]
-#
-# [+Created:+] 03/09/2014
-# [+Copyright:+] Digital Curation Centre and University of California Curation Center
-
-ActiveAdmin.register Organisation do
-	permit_params :abbreviation, :banner_file_id, :description, :logo_file_id, :name, :target_url, :organisation_type_id, :wayfless_entity, :parent_id
-
-	 menu :priority => 14, :label => proc{I18n.t('admin.org')}, :parent => "Organisations management"
-
-	index do
-        column I18n.t('admin.org_title'), :sortable => :name do |ggn|
-            link_to ggn.name, [:admin, ggn]
-        end
-        column I18n.t('admin.abbrev'), :sortable => :abbreviation do |ggn|
-            if !ggn.abbreviation.nil?
-                link_to ggn.abbreviation, [:admin, ggn]
-            else
-                '-'
-            end
-        end
-        column I18n.t('admin.org_type'), :sortable => :organisation_type_id do |org_type|
-            if !org_type.organisation_type_id.nil? then
-                link_to org_type.organisation_type.name, [:admin, org_type]
-            end
-        end
-
-         actions
-    end
-
-
-    #show details of an organisation
-    show do
-        resource.check_api_credentials
-		attributes_table do
-			row I18n.t('admin.org_title'), :sortable => :name do |gn|
-				if !gn.name.nil? then
-                    link_to gn.name, [:admin, gn]
-                end
-            end
-			row I18n.t('admin.abbrev'), :abbreviation do |ggn|
-                if !ggn.abbreviation.nil?
-                    link_to ggn.abbreviation, [:admin, ggn]
-                else
-                    '-'
-                end
-			end
-			row :sort_name
-			row I18n.t('admin.org_type'), :organisation_type_id do |org_type|
-				if !org_type.organisation_type_id.nil? then
-                    link_to org_type.organisation_type.name, [:admin, org_type]
-                end
-            end
-            row :banner_text do |banner|
-                if !banner.banner_text.nil? then
-                    banner.banner_text.html_safe
-                end
-            end
-        #    row :target_url
-            row :logo_file_name
-            row :wayfless_entity
-            row I18n.t('admin.token_permission_type') do
-                (organisation.token_permission_types.map{|tpt| link_to tpt.token_type, [:admin, tpt]}).join(', ').html_safe
-            end
-            row :created_at
-            row :updated_at
-		end
-	end
-
-	#templates sidebar
- 	sidebar I18n.t('admin.templates'), :only => :show, :if => proc { organisation.dmptemplates.count >= 1} do
-	 	table_for organisation.dmptemplates.order("title asc") do |temp|
-	 		column :title do |dmptemp|
-                link_to dmptemp.title, [:admin, dmptemp]
-            end
-            column :published
-	 	end
-	end
-
-	#form
-    form do |f|
-        f.inputs "Details" do
-            f.input :name
-            f.input :abbreviation
-            f.input :sort_name
-            f.input :organisation_type_id, :label => I18n.t('admin.org_type'), :as => :select, :collection => OrganisationType.order('name').map{|orgt|[orgt.name, orgt.id]}
-        #    f.input :target_url
-            f.input :banner_text
-            f.input :logo_file_name
-            f.input :wayfless_entity
-            f.input :token_permission_types, label: I18n.t('admin.token_permission_type'),
-                    as: :select, multiple: true, include_blank: I18n.t('helpers.none'),
-                    collection: TokenPermissionType.order(:token_type).map{|token| [token.token_type, token.id]},
-                    hint: I18n.t('admin.choose_api_permissions')
-        #    f.input :parent_id, :label => I18n.t('admin.org_parent'), :as => :select, :collection => Organisation.find(:all, :order => 'name ASC').map{|orgp|[orgp.name, orgp.id]}
-        #    f.input :stylesheet_file_id
-        end
-        f.actions
-    end
-
-
-	 controller do
-		def permitted_params
-		  params.permit!
-		end
-  end
-
-
-end
diff --git a/app/models/guidance_group.rb b/app/models/guidance_group.rb
index d9102a4..c5cdbe2 100644
--- a/app/models/guidance_group.rb
+++ b/app/models/guidance_group.rb
@@ -2,7 +2,7 @@
   include GlobalHelpers
 
   #associations between tables
-  belongs_to :organisation
+  belongs_to :org
 
   has_and_belongs_to_many :guidances, join_table: "guidance_in_group"
 
diff --git a/app/models/new_answer.rb b/app/models/new_answer.rb
deleted file mode 100644
index e8dd797..0000000
--- a/app/models/new_answer.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-class NewAnswer < ActiveRecord::Base
-  belongs_to :new_plan
-  belongs_to :new_question
-  has_and_belongs_to_many :question_options, join_table: "new_answers_question_options"
-  has_many :notes
-  belongs_to :user
-end
diff --git a/app/models/new_phase.rb b/app/models/new_phase.rb
deleted file mode 100644
index 1919787..0000000
--- a/app/models/new_phase.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-class NewPhase < ActiveRecord::Base
-  belongs_to :template
-  has_many :new_sections
-end
diff --git a/app/models/new_plan.rb b/app/models/new_plan.rb
deleted file mode 100644
index 70b8ca2..0000000
--- a/app/models/new_plan.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-class NewPlan < ActiveRecord::Base
-  has_one :template
-  has_many :roles
-end
diff --git a/app/models/new_question.rb b/app/models/new_question.rb
deleted file mode 100644
index 3935fba..0000000
--- a/app/models/new_question.rb
+++ /dev/null
@@ -1,8 +0,0 @@
-class NewQuestion < ActiveRecord::Base
-  belongs_to :new_section
-  has_one :new_answer
-  has_one :note
-  has_many :question_options
-  belongs_to :question_format
-  has_and_belongs_to_many :themes, join_table: :new_questions_themes
-end
diff --git a/app/models/new_section.rb b/app/models/new_section.rb
deleted file mode 100644
index 4c5c155..0000000
--- a/app/models/new_section.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-class NewSection < ActiveRecord::Base
-  belongs_to :new_phase
-  has_many :new_questions
-end
diff --git a/app/models/new_suggested_answer.rb b/app/models/new_suggested_answer.rb
deleted file mode 100644
index 6578f1d..0000000
--- a/app/models/new_suggested_answer.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-class NewSuggestedAnswer < ActiveRecord::Base
-  belongs_to :new_question
-  belongs_to :organisation
-end
diff --git a/app/models/note.rb b/app/models/note.rb
index 681fee3..66c835f 100644
--- a/app/models/note.rb
+++ b/app/models/note.rb
@@ -1,4 +1,4 @@
 class Note < ActiveRecord::Base
-  belongs_to :new_answer
+  belongs_to :answer
   belongs_to :user
 end
diff --git a/app/models/org.rb b/app/models/org.rb
new file mode 100644
index 0000000..8d81f61
--- /dev/null
+++ b/app/models/org.rb
@@ -0,0 +1,178 @@
+class Org < ActiveRecord::Base
+  include GlobalHelpers
+  
+  extend Dragonfly::Model::Validations
+
+  #associations between tables
+  belongs_to :organisation_type
+  has_many :guidance_groups
+  has_many :templates
+  has_many :users
+  has_many :suggested_answers
+  has_and_belongs_to_many :token_permission_types, join_table: "org_token_permissions"
+
+  belongs_to :parent, :class_name => 'Organisation'
+
+	belongs_to :language
+
+	has_many :children, :class_name => 'Organisation', :foreign_key => 'parent_id'
+
+	accepts_nested_attributes_for :templates
+  accepts_nested_attributes_for :token_permission_types
+
+	attr_accessible :abbreviation, :banner_text, :logo, :remove_logo,
+                  :logo_file_name, :name, :target_url,
+                  :organisation_type_id, :wayfless_entity, :parent_id, :sort_name,
+                  :token_permission_type_ids, :language_id, :contact_email
+
+  validates :contact_email, email: true, allow_nil: true
+  validates :name, presence: true, uniqueness: true
+
+  # allow validations for logo upload
+  dragonfly_accessor :logo do
+    after_assign :resize_image
+  end
+  
+  validates_property :height, of: :logo, in: (0..100)
+  validates_property :format, of: :logo, in: ['jpeg', 'png', 'gif','jpg','bmp']
+  validates_size_of :logo, maximum: 500.kilobytes
+
+  ##
+  # returns the name of the organisation
+  #
+  # @return [String]
+  def to_s
+    name
+  end
+
+  ##
+  # returns the abbreviation for the organisation if it exists, or the name if not
+  #
+  # @return [String] name or abbreviation of the organisation
+  def short_name
+    if abbreviation.nil? then
+      return name
+    else
+      return abbreviation
+    end
+  end
+
+  ##
+  # finds all organisations who have a parent of the passed organisation type
+  #
+  # @param [String] the name of an organisation type
+  # @return [Array<Organisation>]
+  def self.orgs_with_parent_of_type(org_type)
+    parents = OrganisationType.find_by_name(org_type).organisations
+    children = Array.new
+    parents.each do |parent|
+        children += parent.children
+    end
+    return children
+  end
+
+  ##
+  # returns a list of all guidance groups belonging to other organisations
+  #
+  # @return [Array<GuidanceGroup>]
+  def self.other_organisations
+    org_types = [GlobalHelpers.constant("organisation_types.funder")]
+    organisations_list = []
+    org_types.each do |ot|
+      new_org_obejct = OrganisationType.find_by_name(ot)
+
+      org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
+
+      organisations_list = organisations_list + org_with_guidance
+    end
+    return organisations_list
+  end
+
+
+  ##
+  # returns a list of all guidance groups belonging to other organisations
+  #
+  # @return [Array<GuidanceGroup>]
+	def self.other_organisations
+		org_types = [GlobalHelpers.constant("organisation_types.funder")]
+		organisations_list = []
+		org_types.each do |ot|
+			new_org_obejct = OrganisationType.find_by_name(ot)
+
+			org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
+
+			organisations_list = organisations_list + org_with_guidance
+		end
+		return organisations_list
+	end
+
+  ##
+  # returns a list of all sections of a given version from this organisation and it's parents
+  #
+  # @param version_id [Integer] version number of the section
+  # @return [Array<Section>] list of sections
+	def all_sections(version_id)
+		if parent.nil?
+			secs = sections.where("version_id = ?", version_id)
+			if secs.nil? then
+				secs = Array.new
+			end
+			return secs
+		else
+			return sections.where("version_id = ? ", version_id).all + parent.all_sections(version_id)
+		end
+	end
+
+  ##
+  # returns the guidance groups of this organisation and all of it's children
+  #
+  # @return [Array<GuidanceGroup>] list of guidance groups
+	def all_guidance_groups
+		ggs = guidance_groups
+		children.each do |c|
+			ggs = ggs + c.all_guidance_groups
+		end
+		return ggs
+	end
+
+  ##
+  # returns the highest parent organisation in the tree
+  #
+  # @return [organisation] the root organisation
+	def root
+		if parent.nil?
+			return self
+		else
+			return parent.root
+		end
+	end
+
+  ##
+  # returns all published templates belonging to the organisation
+  #
+  # @return [Array<Dmptemplate>] published dmptemplates
+	def published_templates
+		return dmptemplates.where("published = ?", true)
+	end
+
+  def check_api_credentials
+    if token_permission_types.count == 0
+      users.each do |user|
+        user.api_token = ""
+        user.save!
+      end
+    end
+  end
+  
+  private
+    ##
+    # checks size of logo and resizes if necessary
+    #
+    def resize_image
+      unless logo.nil?
+        if logo.height != 100
+          self.logo = logo.thumb('x100')  # resize height and maintain aspect ratio
+        end
+      end
+    end 
+end
diff --git a/app/models/organisation.rb b/app/models/organisation.rb
deleted file mode 100644
index 14c5672..0000000
--- a/app/models/organisation.rb
+++ /dev/null
@@ -1,179 +0,0 @@
-class Organisation < ActiveRecord::Base
-  include GlobalHelpers
-  
-  extend Dragonfly::Model::Validations
-
-  #associations between tables
-  belongs_to :organisation_type
-  has_many :guidance_groups
-  has_many :dmptemplates
-  has_many :sections
-  has_many :users
-  has_many :suggested_answers
-  has_and_belongs_to_many :token_permission_types, join_table: "org_token_permissions"
-
-  belongs_to :parent, :class_name => 'Organisation'
-
-	has_one :language
-
-	has_many :children, :class_name => 'Organisation', :foreign_key => 'parent_id'
-
-	accepts_nested_attributes_for :dmptemplates
-  accepts_nested_attributes_for :token_permission_types
-
-	attr_accessible :abbreviation, :banner_text, :logo, :remove_logo,
-                  :logo_file_name, :name, :target_url,
-                  :organisation_type_id, :wayfless_entity, :parent_id, :sort_name,
-                  :token_permission_type_ids, :language_id, :contact_email
-
-  validates :contact_email, email: true, allow_nil: true
-  validates :name, presence: true, uniqueness: true
-
-  # allow validations for logo upload
-  dragonfly_accessor :logo do
-    after_assign :resize_image
-  end
-  
-  validates_property :height, of: :logo, in: (0..100)
-  validates_property :format, of: :logo, in: ['jpeg', 'png', 'gif','jpg','bmp']
-  validates_size_of :logo, maximum: 500.kilobytes
-
-  ##
-  # returns the name of the organisation
-  #
-  # @return [String]
-  def to_s
-    name
-  end
-
-  ##
-  # returns the abbreviation for the organisation if it exists, or the name if not
-  #
-  # @return [String] name or abbreviation of the organisation
-  def short_name
-    if abbreviation.nil? then
-      return name
-    else
-      return abbreviation
-    end
-  end
-
-  ##
-  # finds all organisations who have a parent of the passed organisation type
-  #
-  # @param [String] the name of an organisation type
-  # @return [Array<Organisation>]
-  def self.orgs_with_parent_of_type(org_type)
-    parents = OrganisationType.find_by_name(org_type).organisations
-    children = Array.new
-    parents.each do |parent|
-        children += parent.children
-    end
-    return children
-  end
-
-  ##
-  # returns a list of all guidance groups belonging to other organisations
-  #
-  # @return [Array<GuidanceGroup>]
-  def self.other_organisations
-    org_types = [GlobalHelpers.constant("organisation_types.funder")]
-    organisations_list = []
-    org_types.each do |ot|
-      new_org_obejct = OrganisationType.find_by_name(ot)
-
-      org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
-
-      organisations_list = organisations_list + org_with_guidance
-    end
-    return organisations_list
-  end
-
-
-  ##
-  # returns a list of all guidance groups belonging to other organisations
-  #
-  # @return [Array<GuidanceGroup>]
-	def self.other_organisations
-		org_types = [GlobalHelpers.constant("organisation_types.funder")]
-		organisations_list = []
-		org_types.each do |ot|
-			new_org_obejct = OrganisationType.find_by_name(ot)
-
-			org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
-
-			organisations_list = organisations_list + org_with_guidance
-		end
-		return organisations_list
-	end
-
-  ##
-  # returns a list of all sections of a given version from this organisation and it's parents
-  #
-  # @param version_id [Integer] version number of the section
-  # @return [Array<Section>] list of sections
-	def all_sections(version_id)
-		if parent.nil?
-			secs = sections.where("version_id = ?", version_id)
-			if secs.nil? then
-				secs = Array.new
-			end
-			return secs
-		else
-			return sections.where("version_id = ? ", version_id).all + parent.all_sections(version_id)
-		end
-	end
-
-  ##
-  # returns the guidance groups of this organisation and all of it's children
-  #
-  # @return [Array<GuidanceGroup>] list of guidance groups
-	def all_guidance_groups
-		ggs = guidance_groups
-		children.each do |c|
-			ggs = ggs + c.all_guidance_groups
-		end
-		return ggs
-	end
-
-  ##
-  # returns the highest parent organisation in the tree
-  #
-  # @return [organisation] the root organisation
-	def root
-		if parent.nil?
-			return self
-		else
-			return parent.root
-		end
-	end
-
-  ##
-  # returns all published templates belonging to the organisation
-  #
-  # @return [Array<Dmptemplate>] published dmptemplates
-	def published_templates
-		return dmptemplates.where("published = ?", true)
-	end
-
-  def check_api_credentials
-    if token_permission_types.count == 0
-      users.each do |user|
-        user.api_token = ""
-        user.save!
-      end
-    end
-  end
-  
-  private
-    ##
-    # checks size of logo and resizes if necessary
-    #
-    def resize_image
-      unless logo.nil?
-        if logo.height != 100
-          self.logo = logo.thumb('x100')  # resize height and maintain aspect ratio
-        end
-      end
-    end 
-end
diff --git a/app/models/phase.rb b/app/models/phase.rb
index 155a86f..c56d091 100644
--- a/app/models/phase.rb
+++ b/app/models/phase.rb
@@ -8,14 +8,11 @@
 	extend FriendlyId
 
 	#associations between tables
-	belongs_to :dmptemplate
-
-	has_many :versions, :dependent => :destroy
-	has_many :sections, :through => :versions, :dependent => :destroy
+	belongs_to :template
+	has_many :sections, :dependent => :destroy
   has_many :questions, :through => :sections, :dependent => :destroy
 
 	#Link the child's data
-	accepts_nested_attributes_for :versions, :allow_destroy => true 
 #	accepts_nested_attributes_for :dmptemplate
 
 	attr_accessible :description, :number, :title, :dmptemplate_id, :as => [:default, :admin]
diff --git a/app/models/role.rb b/app/models/role.rb
index ea6573c..02caf1b 100644
--- a/app/models/role.rb
+++ b/app/models/role.rb
@@ -1,4 +1,4 @@
 class Role < ActiveRecord::Base
   belongs_to :user
-  belongs_to :new_plan
+  belongs_to :plan
 end
diff --git a/app/models/suggested_answer.rb b/app/models/suggested_answer.rb
index 3bbefa8..56376db 100644
--- a/app/models/suggested_answer.rb
+++ b/app/models/suggested_answer.rb
@@ -1,6 +1,6 @@
 class SuggestedAnswer < ActiveRecord::Base
 
-	belongs_to :organisation
+	belongs_to :org
 	belongs_to :question
 
 #	accepts_nested_attributes_for :question
diff --git a/app/models/template.rb b/app/models/template.rb
index cb586f6..b3deec8 100644
--- a/app/models/template.rb
+++ b/app/models/template.rb
@@ -1,5 +1,5 @@
 class Template < ActiveRecord::Base
-  belongs_to :organisation
+  belongs_to :org
   has_many :new_phases
   has_many :new_plans
 end
diff --git a/app/models/user.rb b/app/models/user.rb
index c0595e9..6a14c60 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -13,7 +13,7 @@
     has_many :user_role_types, through: :user_org_roles
     belongs_to :language
 
-    belongs_to :organisation
+    belongs_to :org
 
     has_many :projects, through: :project_groups do
       def filter(query)
diff --git a/app/models/users_perm.rb b/app/models/users_perm.rb
new file mode 100644
index 0000000..38a6cd3
--- /dev/null
+++ b/app/models/users_perm.rb
@@ -0,0 +1,4 @@
+class UsersPerm < ActiveRecord::Base
+  belongs_to :user
+  belongs_to :perm
+end
\ No newline at end of file
diff --git a/config/routes.rb b/config/routes.rb
index 78c801a..925af56 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -42,7 +42,7 @@
     #post 'contact_form' => 'contacts', as: 'localized_contact_creation'
     #get 'contact_form' => 'contacts#new', as: 'localized_contact_form'
     
-    resources :organisations, :path => 'org/admin', only: [] do
+    resources :orgs, :path => 'org/admin', only: [] do
       member do
         get 'children'
         get 'templates'
diff --git a/db/migrate/20161205095623_removing_intermediary_tables.rb b/db/migrate/20161205095623_removing_intermediary_tables.rb
index 18a698e..79f2f4f 100644
--- a/db/migrate/20161205095623_removing_intermediary_tables.rb
+++ b/db/migrate/20161205095623_removing_intermediary_tables.rb
@@ -1,5 +1,5 @@
 class RemovingIntermediaryTables < ActiveRecord::Migration
-  def change
+  def up
     # removing intermediary structures
 
     drop_table :dmptemplates
@@ -43,7 +43,7 @@
     end
     drop_table :options
 
-    change_table :answers_question_options do |t|
+    change_table :new_answers_question_options do |t|
       t.rename :new_answer_id, :answer_id
     end
     drop_table :answers_options
@@ -66,5 +66,87 @@
     change_table :new_suggested_answers do |t|
       t.rename :new_question_id, :question_id
     end
+    drop_table :suggested_answers
+    rename_table :new_suggested_answers, :suggested_answers
+
+    #drop_table :projects
+
+    #rename_table :organisations, :orgs
+    rename_column :guidance_groups, :organisation_id, :org_id
+    rename_column :suggested_answers, :organisation_id, :org_id
+    rename_column :org_token_permissions, :organisation_id, :org_id
+    rename_column :projects, :organisation_id, :org_id
+    rename_column :templates, :organisation_id, :org_id
+    rename_column :users, :organisation_id, :org_id
+
+  end
+
+  def down
+    create_table :dmptemplates
+    change_table :phases do |t|
+      t.integer :vid
+    end
+    rename_table :phases, :new_phases
+    create_table :phases
+
+
+    change_table :sections do |t|
+      t.rename :phase_id, :new_phase_id
+    end
+    rename_table :sections, :new_sections
+    create_table :sections
+
+
+    change_table :questions do |t|
+      t.rename :section_id, :new_section_id
+      t.integer :question_id
+    end
+    rename_table :questions, :new_questions
+    create_table :questions
+
+    change_table :questions_themes do |t|
+      t.rename :question_id, :new_question_id
+    end
+    rename_table :questions_themes, :new_questions_themes
+    create_table :questions_themes
+
+    change_table :answers do |t|
+      t.rename :plan_id, :new_plan_id
+      t.rename :question_id, :new_question_id
+    end
+    rename_table :answers, :new_answers
+    create_table :answers
+
+    change_table :question_options do |t|
+      t.rename :question_id, :new_question_id
+      t.integer :option_id
+    end
+    create_table :options
+
+    change_table :answers_question_options do |t|
+      t.rename :answer_id, :new_answer_id
+    end
+    rename_table :answers_question_options, :new_answers_question_options
+    create_table :answers_options
+
+    change_table :notes do |t|
+      t.rename :answer_id, :new_answer_id
+    end
+    create_table :comments
+
+    change_table :plans do |t|
+    end
+    rename_table :plans, :new_plans
+    create_table :plans
+
+    change_table :roles do |t|
+      t.rename :plan_id, :new_plan_id
+    end
+
+    rename_table  :suggested_answers, :new_suggested_answers
+    create_table :suggested_answers
+    change_table :new_suggested_answers do |t|
+      t.rename :question_id, :new_question_id
+    end
   end
 end
diff --git a/db/migrate/20161206122926_add_foreign_keys.rb b/db/migrate/20161206122926_add_foreign_keys.rb
new file mode 100644
index 0000000..d071ad5
--- /dev/null
+++ b/db/migrate/20161206122926_add_foreign_keys.rb
@@ -0,0 +1,227 @@
+class AddForeignKeys < ActiveRecord::Migration
+    # this migraiton modifies data in tables, and thus depends on being at a specific
+    # point in the history of the codebase.  Specificly the models must reflect the
+    # relationships expected within this code
+  def change
+    # remove broken references
+    scrub_references
+    # answers
+    add_foreign_key :answers, :users
+    add_foreign_key :answers, :plans
+    add_foreign_key :answers, :questions
+
+    # answers_question_options
+    add_foreign_key :answers_question_options, :answers
+    add_foreign_key :answers_question_options, :question_options
+
+    # notes
+    add_foreign_key :notes, :answers
+    add_foreign_key :notes, :users
+
+    # templates
+    add_foreign_key :templates, :orgs
+
+    # guidance_groups
+    add_foreign_key :guidance_groups, :orgs
+
+    # guidance_in_group
+    add_foreign_key :guidance_in_group, :guidance_groups
+    add_foreign_key :guidance_in_group, :guidances
+
+    # guidances
+    add_foreign_key :guidances, :guidance_groups
+
+    # question_options
+    add_foreign_key :question_options, :questions
+
+    # org_token_permissions
+    add_foreign_key :org_token_permissions, :orgs
+    add_foreign_key :org_token_permissions, :token_permission_types
+
+    # orgs
+    add_foreign_key :orgs, :regions
+    add_foreign_key :orgs, :languages
+
+    # phases
+    add_foreign_key :phases, :templates
+
+    # plans
+    add_foreign_key :plans, :templates
+
+    # roles
+    add_foreign_key :roles, :plans
+    add_foreign_key :roles, :users
+
+    # questions
+    add_foreign_key :questions, :sections
+    add_foreign_key :questions, :question_formats
+
+    # questions_themes
+    add_foreign_key :questions_themes, :questions
+    add_foreign_key :questions_themes, :themes
+
+    # sections
+    add_foreign_key :sections, :phases
+
+    # suggested_answers
+    add_foreign_key :suggested_answers, :orgs
+    add_foreign_key :suggested_answers, :questions
+
+    # themes_in_guidance
+    add_foreign_key :themes_in_guidance, :themes
+    add_foreign_key :themes_in_guidance, :guidances
+
+    # users
+    add_foreign_key :users, :orgs
+    add_foreign_key :users, :languages
+
+    # users_perms
+    add_foreign_key :users_perms, :users
+    add_foreign_key :users_perms, :perms
+  end
+
+  def scrub_references
+    # answers
+    i = 0
+    Answer.includes(:user, :plan, :question).find_each do |ans|
+      if ans.user.nil? && ans.user_id.present?
+        ans.user_id = nil
+        i += 1
+      end
+      if ans.plan.nil? && ans.plan_id.present?
+        ans.plan_id = nil
+        i += 1
+      end
+      if ans.question.nil? && ans.question_id.present?
+        ans.question_id = nil
+        i += 1
+      end
+      ans.save!
+    end
+    puts "#{i} answers scrubbed"
+
+    # notes
+    i = 0
+    Note.includes(:answer, :user).find_each do |note|
+      if note.answer.nil? && note.answer_id.present?
+        note.answer_id = nil
+        i += 1
+      end
+      if note.user.nil? && note.user_id.present?
+        note.user_id = nil
+        i += 1
+      end
+      note.save!
+    end
+    puts "#{i} notes scrubbed"
+
+    # templates
+    i = 0
+    Template.includes(:org).find_each do |temp|
+      if temp.org.nil? && temp.org_id.present?
+        temp.org_id = nil
+        i += 1
+      end
+      temp.save!
+    end
+    puts "#{i} templates scrubbed"
+
+    # guidance_groups
+    # i = 0
+    # GuidanceGroup.includes(:org).find_each do |gg|
+    #   if gg.org.nil? && gg.org_id.present?
+    #     gg.org_id = nil
+    #     i += 1
+    #   end
+    #   gg.save!
+    # end
+    # puts "#{i} guidance groups scrubbed"
+
+    # # question_options
+    # i = 0
+    # QuestionOption.includes(:question).find_each do |opt|
+    #   if opt.question.nil? && opt.question_id.present?
+    #     opt.question_id = nil
+    #     i += 1
+    #   end
+    #   opt.save!
+    # end
+    # puts "#{i} question_options scrubbed"
+
+    # # orgs
+    # i = 0
+    # Org.includes( :language).find_each do |org|
+    #   if org.language.nil? && org.language_id.present?
+    #     org.language_id = nil
+    #     i += 1
+    #   end
+    #   org.save!
+    # end
+    # puts "#{i} orgs scrubbed"
+
+    # # phases
+    # # new structure so it's fine
+
+    # # plans
+    # # new structure so it's fine
+
+    # # roles
+    # i = 0
+    # Role.includes(:user, :plan).find_each do |role|
+    #   if role.user.nil? && role.user_id.present?
+    #     role.delete!
+    #     i += 1
+    #     next
+    #   end
+    #   if role.plan.nil? && role.plan_id.present?
+    #     role.delete!
+    #     i += 1
+    #   end
+    # end
+    # puts "#{i} roles scrubbed"
+
+    # # questions
+
+    # # sections
+
+    # # suggested_answers
+    # i = 0
+    # SuggestedAnswer.includes(:org, :question).find_each do |sa|
+    #   if sa.org.nil? && sa.org_id.present?
+    #     sa.org_id = nil
+    #     i += 1
+    #   end
+    #   if sa.question.nil?
+    #     sa.delete!
+    #     i += 1
+    #     next
+    #   end
+    #   sa.save!
+    # end
+    # puts "#{i} suggested answers scrubbed"
+
+    # # themes_in_guidance
+
+    # # users
+    # i = 0
+    # User.includes(:org, :language).find_each do |u|
+    #   if u.org.nil? && u.org_id.present?
+    #     u.org_id = nil
+    #     i += 1
+    #   end
+    #   if u.language.nil? && u.language_id.present?
+    #     u.language_id = nil
+    #     i += 1
+    #   end
+    #   u.save!
+    # end
+    # puts "#{i} users scrubbed"
+
+    # users_perms
+    UsersPerm.includes(:user).all.each do |u|
+      if u.user.nil?
+        UsersPerm.delete_all(user_id: u.user_id)
+      end
+    end
+  end
+end