SELECT manifest, versionId, max(checkinTime)
FROM version
GROUP BY manifest, versionId
ORDER BY 3 DESC LIMIT 1;
or
WITH m AS (SELECT max(checkinTime) AS checkinTime FROM version)
SELECT v.manifest, v.versionId, v.checkinTime
FROM version v
JOIN m m USING (checkinTime)
LIMIT 1;
It's a bit of a footgun though because there is some randomness here if multiple rows have the same max checkinTime, so I try not to use this SQLite3-ism. You want to also do something to deterministically pick a "best" row, but for that you need to do something like the above.