Handle orphans when removing soft deleted groups

There may be more tables but these were the tables that were problematic
for GitLab.com due to foreign key constraints (without cascading
deletes).

db/migrate/20161117114805_remove_undeleted_groups.rb

@@ -5,6 +5,47 @@ class RemoveUndeletedGroups < ActiveRecord::Migration
   DOWNTIME = false
 
   def up
+    execute <<-EOF.strip_heredoc
+    DELETE FROM projects
+    WHERE namespace_id IN (
+      SELECT id FROM (
+        SELECT id
+        FROM namespaces
+        WHERE deleted_at IS NOT NULL
+      ) namespace_ids
+    );
+    EOF
+
+    if defined?(Gitlab::License)
+      # EE adds these columns but we have to make sure this data is cleaned up
+      # here before we run the DELETE below. An alternative would be patching
+      # this migration in EE but this will only result in a mess and confusing
+      # migrations.
+      execute <<-EOF.strip_heredoc
+      DELETE FROM protected_branch_push_access_levels
+      WHERE group_id IN (
+        SELECT id FROM (
+          SELECT id
+          FROM namespaces
+          WHERE deleted_at IS NOT NULL
+        ) namespace_ids
+      );
+      EOF
+
+      execute <<-EOF.strip_heredoc
+      DELETE FROM protected_branch_merge_access_levels
+      WHERE group_id IN (
+        SELECT id FROM (
+          SELECT id
+          FROM namespaces
+          WHERE deleted_at IS NOT NULL
+        ) namespace_ids
+      );
+      EOF
+    end
+
+    # This removes namespaces that were supposed to be soft deleted but still
+    # reside in the database.
     execute "DELETE FROM namespaces WHERE deleted_at IS NOT NULL;"
   end