Remove old preferences system

For #8751.

This also removes `PreferencesManager.setValueAndSave()`, deprecated by 08e8208e2c2bd229be4e0f11700853890a981c5f in Sprint 37. In order to prevent a repeat of Quick Open, I removed it in a separate commit in case it needs to be reverted and set my search utility to scan more thoroughly. No known extension usage was discovered.

/cc @dangoor  
We should also remove all the usages of this functions in our codebase.