Config fixings

- Delete now really overwrites static default/setting.config.php keys
- Delete now really overwrites static default/setting.config.php categories
- The Update::check() routine is added to different places
- Merge the given config file with the new config before writing
- Remove ConfigTransaction::get() because it's no more reliable

tests/src/Core/Config/ConfigTest.php

@@ -364,7 +364,7 @@ class ConfigTest extends MockedTest
 		self::assertNull($this->testedConfig->get('test', 'it'));
 		self::assertNull($this->testedConfig->getCache()->get('test', 'it'));
 
-		self::assertEmpty($this->testedConfig->getCache()->getAll());
+		self::assertEquals(['test' => null], $this->testedConfig->getCache()->getAll());
 	}
 
 	/**