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Looking at system.services.yaml, I noticed that some of the services arguments are strings starting with @. They seem to contain a reference to another defined service.

system.manager:
class: Drupal\system\SystemManager
arguments: ['@module_handler', '@database', '@entity.manager'] 

Are those @-arguments only references to other services? Are there any other type of arguments I can use when defining a new service?

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Yes, the @ arguments are references to services. From Symfony's Introduction to Parameters:

You can of course also reference services, which looks a bit different in each format. You can configure the behavior if the referenced service does not exist. By default, an exception is thrown when a non-existent service is referenced.

Yaml

Start the string with @ or @? to reference a service in Yaml.

  • @mailer references the mailer service. If the service does not exists, an exception will be thrown;

  • @?mailer references the mailer service. If the service does not exists, it will be ignored;

You can also use %-wrapped parameters which are slightly different; they can be used to refer parameters or get access to special SYMFONY__ prefixed server environment vars. (See How to Set External Parameters in the Service Container.)

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