Thanks to @ashley for providing the awesome list! (her comment is located at https://phabricator.wikimedia.org/T141318#2509624)
To do list
- Remove relevant entries from LocalSettings.php (the switch loop, $bmAllProjects/$wgLocalDatabases variable, $wgConf->settings, the $refreshed<project to be closed> variable,
- Remove relevant entry from $newTalkGlobalDatabases, $wgSiteMatrixSites and $wgLocalDatabases in LocalSettings_ext.php
- Edit other LocalSettings (e.g. LocalSettings_gbc.php and such which are not going to be deleted) to update the $wgRefreshedHeader['dropdown'] variable to remove the removed sites from the drop-down menu (won't be needed if T134669 is (partially) fixed)
- Delete the LocalSettings file for the site(s) to be deleted, e.g. LocalSettings_ideas.php
- Commit these changes to the LocalSettings repository (Brickimedia/LocalSettings on GitHub)
- Deploy new configuration to production