variable_get() has previously handled two classes of things that could be set in $conf:
1. Early bootstrap settings that would never end up in the database, which had to be set in settings.php instead
2. Variables which could live in the database, but might be overridden in $conf.
$conf is now specifically for configuration overrides, so we should find a new place to put things in the first group.
I'd suggest either $settings or $drupal_settings.
There are also some one-off globals, like $update_free_access which we could move into keys of this new global - just to reduce the number of global variables overall.
Major because there are already some CMI conversions which have put things into $conf and we'll need to move them out again.
PASSED: [[SimpleTest]]: [MySQL] 50,493 pass(es).
PASSED: [[SimpleTest]]: [MySQL] 50,491 pass(es).
PASSED: [[SimpleTest]]: [MySQL] 50,504 pass(es).