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Fresh CLI installation bug
From 3.0 through 3.5.7, cli-install.php omitted manager_theme and site_id. The web installer created them because
it passed through installLevel === 4; the CLI installer used a separate path and never executed that block.
Upgrade/backfill bug
The fresh CLI installation bug was fixed in 3.5.8 by adding both settings to install/cli-install.php:606. But
existing CLI-installed sites retained the missing rows because the updater did not backfill them.