New zeitwerk integration breaks existing configuration for loading rails engines

[DanielHeath]

As of 28eae0fc08205c79089bef2b243e70ea35c25e1a , my app (which uses an engine), fails to load on rails (revision b945dfbb69c53c19575fd2c5d42c79ecb21196f7), with:

gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:471:in `block (3 levels) in raise_if_conflicting_directory': loader (Zeitwerk::Error)

#<Zeitwerk::Loader:0x00007f15cd1145b0
 @autoloaded_dirs=[],
 @autoloads={},
 @collapse_dirs=#<Set: {}>,
 @collapse_glob_patterns=#<Set: {}>,
 @eager_load_exclusions=#<Set: {}>,
 @eager_loaded=false,
 @ignored_glob_patterns=#<Set: {}>,
 @ignored_paths=#<Set: {}>,
 @inflector=Rails::Autoloaders::Inflector,
 @initialized_at=2023-01-18 12:20:10.342387947 +1100,
 @logger=nil,
 @mutex=#<Thread::Mutex:0x00007f15cd11e150>,
 @mutex2=#<Thread::Mutex:0x00007f15cd11dd90>,
 @namespace_dirs={},
 @on_load_callbacks={},
 @on_setup_callbacks=[],
 @on_unload_callbacks={},
 @reloading_enabled=false,
 @roots={},
 @setup=true,
 @shadowed_files=#<Set: {}>,
 @tag="rails.once",
 @to_unload={}>


wants to manage directory vendor/cache/dbhero-31065fc1bd42/app/controllers, which is already managed by

<snip for sensitive / long>

	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:465:in `each_key'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:465:in `block (2 levels) in raise_if_conflicting_directory'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:461:in `each'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:461:in `block in raise_if_conflicting_directory'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:458:in `synchronize'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader.rb:458:in `raise_if_conflicting_directory'
	from gems/zeitwerk-2.6.6/lib/zeitwerk/loader/config.rb:123:in `push_dir'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:79:in `block in eager_load_engine'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:75:in `each'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:75:in `eager_load_engine'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:65:in `block (2 levels) in load_rails_engines'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:64:in `each'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:64:in `block in load_rails_engines'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:119:in `with_rails_application'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:63:in `load_rails_engines'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/loader.rb:33:in `load_bundle'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/gem.rb:59:in `require_gem_file'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/gem.rb:33:in `load'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/loaders/gem.rb:27:in `load_application'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/commands/gem.rb:243:in `block in perform_additions'
	from gems/thor-1.2.1/lib/thor/shell/basic.rb:44:in `indent'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/commands/gem.rb:239:in `perform_additions'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/commands/gem.rb:115:in `sync'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/cli.rb:266:in `block in gem'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca.rb:23:in `block in silence_warnings'
	from /home/daniel/.rubies/ruby-3.1.2/lib/ruby/3.1.0/rubygems/user_interaction.rb:46:in `use_ui'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca.rb:22:in `silence_warnings'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `bind_call'
	from gems/sorbet-runtime-0.5.10626/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/lib/tapioca/cli.rb:235:in `gem'
	from gems/thor-1.2.1/lib/thor/command.rb:27:in `run'
	from gems/thor-1.2.1/lib/thor/invocation.rb:127:in `invoke_command'
	from gems/thor-1.2.1/lib/thor.rb:392:in `dispatch'
	from gems/thor-1.2.1/lib/thor/base.rb:485:in `start'
	from <railsapp>/vendor/cache/tapioca-1b485c6ce47f/exe/tapioca:25:in `<top (required)>'
	from bin/tapioca:29:in `load'
	from bin/tapioca:29:in `<main>'