Update https://docs.moodle.org/dev/Moodle_4.0_developer_update to have a section that specifies what theme plugin developers have to do to get their plugins working. Please see MDL-73393 for the specifics of what theme developers need to do. Please also include information about how to fix their problems, such as how to add back the settings cog, or a link to how to include the secondary navigation.

Also please create a forum post pointing to the Moodle 4.0 developer update to help inform more people.