diff --git a/lib/jsduck/batch_processor.rb b/lib/jsduck/batch_processor.rb
index beaf2418546ddf4d017cacaf978e814f1ef6b439..6ae1653696862db4d3b76a78991a39be2614b7c2 100644
--- a/lib/jsduck/batch_processor.rb
+++ b/lib/jsduck/batch_processor.rb
@@ -50,8 +50,7 @@ module JsDuck
       Process::Accessors.new(classes_hash).process_all!
       Process::Ext4Events.new(classes_hash, opts).process_all!
       Process::Enums.new(classes_hash).process_all!
-      # Ignore override classes after applying them to actual classes
-      opts.external_classes += Process::Overrides.new(classes_hash).process_all!
+      Process::Overrides.new(classes_hash, opts).process_all!
 
       classes_hash.values
     end
diff --git a/lib/jsduck/options.rb b/lib/jsduck/options.rb
index ae8f59c6a0755c84676399b22ab559e8846be1ac..1adf53e832dc40a26955af889b60b8fea04f6630 100644
--- a/lib/jsduck/options.rb
+++ b/lib/jsduck/options.rb
@@ -142,7 +142,10 @@ module JsDuck
     # Make options object behave like hash.
     # This allows us to substitute it with hash in unit tests.
     def [](key)
-      send(key)
+      instance_variable_get("@#{key}")
+    end
+    def []=(key, value)
+      instance_variable_set("@#{key}", value)
     end
 
     def parse!(argv)
diff --git a/lib/jsduck/process/overrides.rb b/lib/jsduck/process/overrides.rb
index 753a55f293e12d23fb15ceb5d7f6949f077c31f4..6af8ee2f480ecd1e04b3b1033d01ce41491b0bba 100644
--- a/lib/jsduck/process/overrides.rb
+++ b/lib/jsduck/process/overrides.rb
@@ -4,13 +4,15 @@ module JsDuck
   module Process
 
     class Overrides
-      def initialize(classes_hash)
+      def initialize(classes_hash, opts = {:external_classes => []})
         @classes_hash = classes_hash
+        @opts = opts
       end
 
-      # Applies all override classes to target classes, then deletes the
-      # overrides themselves from classes hash.  Returns names of all
-      # the processed override classes.
+      # Applies all override classes to target classes, then deletes
+      # the overrides themselves from classes hash and adds the names
+      # of all the processed overrides to external_classes list in
+      # options object.
       def process_all!
         overrides = []
 
@@ -26,7 +28,7 @@ module JsDuck
           @classes_hash.delete(cls[:name])
         end
 
-        overrides.map {|c| c[:name] }
+        @opts[:external_classes] += overrides.map {|c| c[:name] }
       end
 
       private