diff --git a/lib/rdoc/code_object.rb b/lib/rdoc/code_object.rb
index 388863b06c..45d6bc8987 100644
--- a/lib/rdoc/code_object.rb
+++ b/lib/rdoc/code_object.rb
@@ -291,19 +291,7 @@ def parent
     return @parent if @parent
     return nil unless @parent_name
 
-    if @parent_class == RDoc::TopLevel then
-      @parent = @store.add_file @parent_name
-    else
-      @parent = @store.find_class_or_module @parent_name
-
-      return @parent if @parent
-
-      begin
-        @parent = @store.load_class @parent_name
-      rescue RDoc::Store::MissingFileError
-        nil
-      end
-    end
+    @parent = @store&.resolve_parent(@parent_name, @parent_class)
   end
 
   ##
@@ -361,6 +349,10 @@ def stop_doc
   def store=(store)
     @store = store
 
+    # When a CodeObject is loaded from Marshal data, its @file is a standalone
+    # TopLevel that needs to be replaced with the canonical one from the store.
+    @file = @store.add_file @file.full_name if @file && @store
+
     return unless @track_visibility
 
     if :nodoc == options.visibility then
diff --git a/lib/rdoc/code_object/any_method.rb b/lib/rdoc/code_object/any_method.rb
index f56110ea11..f63c31bf2d 100644
--- a/lib/rdoc/code_object/any_method.rb
+++ b/lib/rdoc/code_object/any_method.rb
@@ -306,15 +306,6 @@ def skip_description?
     has_call_seq? && call_seq.nil? && !!(is_alias_for || !aliases.empty?)
   end
 
-  ##
-  # Sets the store for this method and its referenced code objects.
-
-  def store=(store)
-    super
-
-    @file = @store.add_file @file.full_name if @file
-  end
-
   ##
   # For methods that +super+, find the superclass method that would be called.
 
diff --git a/lib/rdoc/code_object/class_module.rb b/lib/rdoc/code_object/class_module.rb
index 00e406b1a6..43c64a229c 100644
--- a/lib/rdoc/code_object/class_module.rb
+++ b/lib/rdoc/code_object/class_module.rb
@@ -702,12 +702,12 @@ def remove_nodoc_children
 
     modules_hash.each_key do |name|
       full_name = prefix + name
-      modules_hash.delete name unless @store.modules_hash[full_name]
+      modules_hash.delete name unless @store.find_module_named(full_name)
     end
 
     classes_hash.each_key do |name|
       full_name = prefix + name
-      classes_hash.delete name unless @store.classes_hash[full_name]
+      classes_hash.delete name unless @store.find_class_named(full_name)
     end
   end
 
@@ -875,7 +875,7 @@ def update_aliases
   def update_includes
     includes.reject! do |include|
       mod = include.module
-      !(String === mod) && @store.modules_hash[mod.full_name].nil?
+      !(String === mod) && @store.find_module_named(mod.full_name).nil?
     end
 
     includes.uniq!
@@ -891,7 +891,7 @@ def update_extends
     extends.reject! do |ext|
       mod = ext.module
 
-      !(String === mod) && @store.modules_hash[mod.full_name].nil?
+      !(String === mod) && @store.find_module_named(mod.full_name).nil?
     end
 
     extends.uniq!
diff --git a/lib/rdoc/code_object/constant.rb b/lib/rdoc/code_object/constant.rb
index 8823b0bd67..8b5c31e4cf 100644
--- a/lib/rdoc/code_object/constant.rb
+++ b/lib/rdoc/code_object/constant.rb
@@ -174,15 +174,6 @@ def pretty_print(q) # :nodoc:
     end
   end
 
-  ##
-  # Sets the store for this class or module and its contained code objects.
-
-  def store=(store)
-    super
-
-    @file = @store.add_file @file.full_name if @file
-  end
-
   def to_s # :nodoc:
     parent_name = parent ? parent.full_name : '(unknown)'
     if is_alias_for
diff --git a/lib/rdoc/code_object/context.rb b/lib/rdoc/code_object/context.rb
index bd42248424..cb573f2a10 100644
--- a/lib/rdoc/code_object/context.rb
+++ b/lib/rdoc/code_object/context.rb
@@ -305,12 +305,11 @@ def add_class(class_type, given_name, superclass = '::Object')
       if full_name =~ /^(.+)::(\w+)$/ then
         name = $2
         ename = $1
-        enclosing = @store.classes_hash[ename] || @store.modules_hash[ename]
+        enclosing = @store.find_class_or_module(ename)
         # HACK: crashes in actionpack/lib/action_view/helpers/form_helper.rb (metaprogramming)
         unless enclosing then
           # try the given name at top level (will work for the above example)
-          enclosing = @store.classes_hash[given_name] ||
-                      @store.modules_hash[given_name]
+          enclosing = @store.find_class_or_module(given_name)
           return enclosing if enclosing
           # not found: create the parent(s)
           names = ename.split('::')
@@ -358,7 +357,7 @@ def add_class(class_type, given_name, superclass = '::Object')
       superclass = nil if superclass == full_name
     end
 
-    klass = @store.classes_hash[full_name]
+    klass = @store.find_class_named(full_name)
 
     if klass then
       # if TopLevel, it may not be registered in the classes:
@@ -384,8 +383,7 @@ def add_class(class_type, given_name, superclass = '::Object')
       else
         klass = class_type.new name, superclass
 
-        enclosing.add_class_or_module(klass, enclosing.classes_hash,
-                                      @store.classes_hash)
+        enclosing.add_class_or_module(klass, enclosing.classes_hash)
       end
     end
 
@@ -395,13 +393,12 @@ def add_class(class_type, given_name, superclass = '::Object')
   end
 
   ##
-  # Adds the class or module +mod+ to the modules or
-  # classes Hash +self_hash+, and to +all_hash+ (either
-  # <tt>TopLevel::modules_hash</tt> or <tt>TopLevel::classes_hash</tt>),
+  # Adds the class or module +mod+ to the local Hash +self_hash+,
+  # and registers it with the store,
   # unless #done_documenting is +true+. Sets the #parent of +mod+
   # to +self+, and its #section to #current_section. Returns +mod+.
 
-  def add_class_or_module(mod, self_hash, all_hash)
+  def add_class_or_module(mod, self_hash)
     mod.section = current_section # TODO declaring context? something is
                                   # wrong here...
     mod.parent = self
@@ -412,7 +409,11 @@ def add_class_or_module(mod, self_hash, all_hash)
       self_hash[mod.name] = mod
       # this must be done AFTER adding mod to its parent, so that the full
       # name is correct:
-      all_hash[mod.full_name] = mod
+      if mod.module? then
+        @store.modules_hash[mod.full_name] = mod
+      else
+        @store.classes_hash[mod.full_name] = mod
+      end
       if @store.unmatched_constant_alias[mod.full_name] then
         to, file = @store.unmatched_constant_alias[mod.full_name]
         add_module_alias mod, mod.name, to, file
@@ -508,16 +509,16 @@ def add_module(class_type, name)
     return mod if mod
 
     full_name = child_name name
-    mod = @store.modules_hash[full_name] || class_type.new(name)
+    mod = @store.find_module_named(full_name) || class_type.new(name)
 
-    add_class_or_module mod, @modules, @store.modules_hash
+    add_class_or_module mod, @modules
   end
 
   ##
   # Adds a module by +RDoc::NormalModule+ instance. See also #add_module.
 
   def add_module_by_normal_module(mod)
-    add_class_or_module mod, @modules, @store.modules_hash
+    add_class_or_module mod, @modules
   end
 
   ##
@@ -1222,8 +1223,9 @@ def upgrade_to_class(mod, class_type, enclosing)
     klass.store = @store
 
     # if it was there, then we keep it even if done_documenting
+    @store.modules_hash.delete mod.full_name
     @store.classes_hash[mod.full_name] = klass
-    enclosing.classes_hash[mod.name]   = klass
+    enclosing.classes_hash[mod.name] = klass
 
     klass
   end
diff --git a/lib/rdoc/code_object/method_attr.rb b/lib/rdoc/code_object/method_attr.rb
index 3169640982..db8664558e 100644
--- a/lib/rdoc/code_object/method_attr.rb
+++ b/lib/rdoc/code_object/method_attr.rb
@@ -147,15 +147,6 @@ def see
     @see
   end
 
-  ##
-  # Sets the store for this class or module and its contained code objects.
-
-  def store=(store)
-    super
-
-    @file = @store.add_file @file.full_name if @file
-  end
-
   def find_see # :nodoc:
     return nil if singleton || is_alias_for
 
@@ -172,7 +163,7 @@ def find_method_or_attribute(name) # :nodoc:
     return nil unless parent.respond_to? :ancestors
 
     searched = parent.ancestors
-    kernel = @store.modules_hash['Kernel']
+    kernel = @store.find_module_named('Kernel')
 
     searched << kernel if kernel &&
       parent != kernel && !searched.include?(kernel)
diff --git a/lib/rdoc/code_object/mixin.rb b/lib/rdoc/code_object/mixin.rb
index e7b37e0941..f3e54d7c4a 100644
--- a/lib/rdoc/code_object/mixin.rb
+++ b/lib/rdoc/code_object/mixin.rb
@@ -77,43 +77,9 @@ def inspect # :nodoc:
 
   def module
     return @module if @module
-
-    # search the current context
     return @name unless parent
-    full_name = parent.child_name(@name)
-    @module = @store.modules_hash[full_name]
-    return @module if @module
-    return @name if @name =~ /^::/
-
-    # search the includes before this one, in reverse order
-    searched = parent.includes.take_while { |i| i != self }.reverse
-    searched.each do |i|
-      inc = i.module
-      next if String === inc
-      full_name = inc.child_name(@name)
-      @module = @store.modules_hash[full_name]
-      return @module if @module
-    end
-
-    # go up the hierarchy of names
-    up = parent.parent
-    while up
-      full_name = up.child_name(@name)
-      @module = @store.modules_hash[full_name]
-      return @module if @module
-      up = up.parent
-    end
-
-    @name
-  end
-
-  ##
-  # Sets the store for this class or module and its contained code objects.
-
-  def store=(store)
-    super
 
-    @file = @store.add_file @file.full_name if @file
+    @module = @store&.resolve_mixin(@name, parent, self) || @name
   end
 
   def to_s # :nodoc:
diff --git a/lib/rdoc/store.rb b/lib/rdoc/store.rb
index 57429e6aad..a2790e1c51 100644
--- a/lib/rdoc/store.rb
+++ b/lib/rdoc/store.rb
@@ -719,6 +719,63 @@ def modules_hash
     @modules_hash
   end
 
+  ##
+  # Resolves a parent CodeObject by +parent_name+ and +parent_class+.
+  # This encapsulates the lazy parent resolution logic: if the parent is a
+  # TopLevel, it is resolved via add_file; otherwise it is looked up in the
+  # class/module registry, falling back to loading from disk.
+
+  def resolve_parent(parent_name, parent_class)
+    if parent_class == RDoc::TopLevel
+      add_file parent_name
+    else
+      find_class_or_module(parent_name) || begin
+        load_class(parent_name)
+      rescue MissingFileError
+        nil
+      end
+    end
+  end
+
+  ##
+  # Resolves a mixin's module reference by walking the namespace hierarchy.
+  # +name+ is the module name to resolve, +parent_context+ is the Context
+  # containing the mixin, and +mixin+ is the Mixin object itself (used to
+  # limit the include search to only includes before this one).
+  #
+  # Returns the resolved RDoc::NormalModule, or nil if not found.
+
+  def resolve_mixin(name, parent_context, mixin)
+    return nil unless parent_context
+
+    # search the current context
+    full_name = parent_context.child_name(name)
+    found = find_module_named(full_name)
+    return found if found
+    return nil if name =~ /^::/
+
+    # search the includes before this one, in reverse order
+    searched = parent_context.includes.take_while { |i| i != mixin }.reverse
+    searched.each do |i|
+      inc = i.module
+      next if String === inc
+      full_name = inc.child_name(name)
+      found = find_module_named(full_name)
+      return found if found
+    end
+
+    # go up the hierarchy of names
+    up = parent_context.parent
+    while up
+      full_name = up.child_name(name)
+      found = find_module_named(full_name)
+      return found if found
+      up = up.parent
+    end
+
+    nil
+  end
+
   ##
   # Returns the RDoc::TopLevel that is a file and has the given +name+
 
diff --git a/test/rdoc/parser/ruby_test.rb b/test/rdoc/parser/ruby_test.rb
index 413de602f8..452ebd961d 100644
--- a/test/rdoc/parser/ruby_test.rb
+++ b/test/rdoc/parser/ruby_test.rb
@@ -2016,8 +2016,8 @@ def test_parse_method_constant
 
     @parser.parse_method m, RDoc::Parser::Ruby::NORMAL, tk, @comment
 
-    assert_empty @store.modules_hash.keys
-    assert_equal %w[M], @store.classes_hash.keys
+    assert_equal %w[M], @store.modules_hash.keys
+    assert_empty @store.classes_hash.keys
   end
 
   def test_parse_method_false