Fix inconsistent indentation between @code - @endcode block in core

This is a follow-up issue to #2975056: broken sample code in deprecation notices for entity.inc functions. While working on that issue it is noticed that we have the inconsistent indentation between @code - @endcode blocks. At some places, the code is indented with 2 spaces but in other places, it is not. Indent code with 2 spaces.

For example:

This

* @code
* $settings['extension_discovery_scan_tests'] = TRUE;
* @endcode

Should be this:

* @code
*   $settings['extension_discovery_scan_tests'] = TRUE;
* @endcode