Fix rb_define_method(singleton_class_of_module, ...) not to change nested module name

[tompng]

Fixes #1440
Always track class and singleton class stored to a variable to @classes.
Otherwise, find_class var_name, class_name called from handle_method will add a new class.

Before:

After:

Minimal reproduction:

VALUE mFoo = rb_define_module("Foo");
VALUE mBar = rb_define_module_under(mFoo, "Bar");
VALUE mBarS = rb_singleton_class(mBar);
rb_define_method(mBarS, "baz", baz, 0);

RDoc::Parser::C#handle_method calls find_class 'mBarS', 'Foo::Bar'.
RDoc::Parser::C#find_class calls @top_level.add_class RDoc::NormalClass, 'Foo::Bar'. This will create ::Bar for some reason and Foo::Bar disappears from generated document.

[kou]

+1