Clean up stale comment_location placeholders after re-parse

When keep_position: true is used during server re-parse, empty placeholder
entries persist in comment_location if the re-parsed file no longer defines
that class. Add Store#cleanup_stale_contributions to remove empty entries
and stale in_files references after all re-parsing is complete. If a class
has no remaining contributions, it is removed from the store.

Author: st0012

lib/rdoc/server.rb

@@ -363,6 +363,8 @@ def reparse_and_refresh(changed_files, removed_files)
             $stderr.puts "Error parsing #{f}: #{e.message}"
           end
         end
+
+        @store.cleanup_stale_contributions
       end
 
       @store.complete(@options.visibility)

lib/rdoc/store.rb

@@ -279,6 +279,35 @@ def clear_file_contributions(relative_name, keep_position: false)
     top_level.classes_or_modules.clear
   end
 
+  ##
+  # Removes stale empty placeholders left by +clear_file_contributions+ with
+  # <tt>keep_position: true</tt>.  After re-parsing, a file may no longer
+  # define a class it previously contributed to, leaving an empty entry in
+  # +comment_location+ and a stale +in_files+ reference.  Call this after
+  # all re-parsing is complete.
+
+  def cleanup_stale_contributions
+    all_classes_and_modules.each do |cm|
+      cm.comment_location.delete_if { |_, comments| comments.empty? }
+      cm.rebuild_comment_from_location
+
+      cm.in_files.select! { |tl| cm.comment_location.key?(tl) ||
+        cm.method_list.any? { |m| m.file == tl } ||
+        cm.attributes.any? { |a| a.file == tl } ||
+        cm.constants.any? { |c| c.file == tl } }
+
+      if cm.in_files.empty?
+        if cm.is_a?(RDoc::NormalModule)
+          @modules_hash.delete(cm.full_name)
+        else
+          @classes_hash.delete(cm.full_name)
+        end
+        cm.parent&.classes_hash&.delete(cm.name)
+        cm.parent&.modules_hash&.delete(cm.name)
+      end
+    end
+  end
+
   ##
   # Make sure any references to C variable names are resolved to the corresponding class.
   #

test/rdoc/rdoc_store_test.rb

@@ -1255,4 +1255,53 @@ def test_clear_file_contributions_keep_position
     assert_equal 'updated comment from a', klass.comment_location[file_a].first.to_s
   end
 
+  def test_cleanup_stale_comment_locations
+    file_a = @s.add_file 'a.rb'
+    file_b = @s.add_file 'b.rb'
+
+    klass = file_a.add_class RDoc::NormalClass, 'StaleClass'
+    klass.record_location file_a
+    klass.record_location file_b
+    file_a.add_to_classes_or_modules klass
+    file_b.add_to_classes_or_modules klass
+
+    klass.add_comment 'comment from a', file_a
+    klass.add_comment 'comment from b', file_b
+
+    # Simulate keep_position clearing followed by re-parse that no longer
+    # defines StaleClass in a.rb (no add_comment called for file_a)
+    @s.clear_file_contributions 'a.rb', keep_position: true
+
+    # Stale placeholder exists
+    assert_equal [], klass.comment_location[file_a]
+
+    # Cleanup should remove the stale entry
+    @s.cleanup_stale_contributions
+
+    assert_not_include klass.comment_location.keys, file_a
+    assert_not_include klass.in_files, file_a
+    assert_includes klass.comment_location.keys, file_b
+    assert_includes klass.in_files, file_b
+  end
+
+  def test_cleanup_stale_contributions_removes_empty_class
+    file_a = @s.add_file 'a.rb'
+
+    klass = file_a.add_class RDoc::NormalClass, 'GoneClass'
+    klass.record_location file_a
+    file_a.add_to_classes_or_modules klass
+
+    klass.add_comment 'comment from a', file_a
+
+    @s.clear_file_contributions 'a.rb', keep_position: true
+
+    # Stale placeholder exists, class still in store
+    assert_includes @s.classes_hash, 'GoneClass'
+
+    @s.cleanup_stale_contributions
+
+    # Class should be removed from store
+    assert_not_include @s.classes_hash, 'GoneClass'
+  end
+
 end