Added comment

lib/cocoapods/installer/analyzer.rb

@@ -242,6 +242,12 @@ module Pod
         aggregate_user_target_uuids = Set.new aggregate_target.user_targets.map(&:uuid)
         embedded_aggregate_targets.each do |embedded_aggregate_target|
           next unless embedded_aggregate_target.user_targets.any? do |embedded_user_target|
+            # You have to ask the host target's project for the host targets of
+            # the embedded target, as opposed to asking user_project for the
+            # embedded targets of the host target. The latter doesn't work when
+            # the embedded target lives in a sub-project. The line below gets
+            # the host target uuids for the embedded target and checks to see if
+            # those match to any of the user_target uuids in the aggregate_target.
             !aggregate_user_target_uuids.intersection(Set.new(aggregate_target.user_project.host_targets_for_embedded_target(embedded_user_target).map(&:uuid))).empty?
           end
           # This embedded target is hosted by the aggregate target's user_target; copy over the non-duplicate pod_targets