Make sure we use compare by identity Sets properly

There have been a few instances where we have not been using `Set`s with `compare_by_identity` properly. This commit fixes those instances so that the test added in the previous commit passes.

Fixes #1728

lib/tapioca/dsl/compiler.rb

@@ -36,7 +36,7 @@ def gather_constants; end
         sig { returns(T::Set[Module]) }
         def processable_constants
           @processable_constants ||= T.let(
-            T::Set[Module].new(gather_constants).compare_by_identity,
+            T::Set[Module].new.compare_by_identity.merge(gather_constants),
             T.nilable(T::Set[Module]),
           )
         end

lib/tapioca/dsl/pipeline.rb

@@ -130,7 +130,10 @@ def gather_active_compilers(requested_compilers, excluded_compilers)
 
       sig { params(requested_constants: T::Array[Module], requested_paths: T::Array[Pathname]).returns(T::Set[Module]) }
       def gather_constants(requested_constants, requested_paths)
-        constants = active_compilers.map(&:processable_constants).reduce(Set.new, :union)
+        constants = Set.new.compare_by_identity
+        active_compilers.each do |compiler|
+          constants.merge(compiler.processable_constants)
+        end
         constants = filter_anonymous_and_reloaded_constants(constants)
 
         constants &= requested_constants unless requested_constants.empty? && requested_paths.empty?
@@ -158,11 +161,12 @@ def filter_anonymous_and_reloaded_constants(constants)
 
         # Look up all the constants back from their names. The resulting constant set will be the
         # set of constants that are actually in memory with those names.
-        constants_by_name
+        filtered_constants = constants_by_name
           .keys
           .map { |name| T.cast(Runtime::Reflection.constantize(name), Module) }
           .select { |mod| Runtime::Reflection.constant_defined?(mod) }
-          .to_set
+
+        Set.new.compare_by_identity.merge(filtered_constants)
       end
 
       sig { params(constant: Module).returns(T.nilable(RBI::File)) }