How to fix? SQLite corrupt, so Meteor CLI is broken

Using sqlite3 you can repair the DB.

cd ~/.meteor/package-metadata/v2.0.1
sqlite3 packages.data.db .dump > backup
mv packages.data.db packages.data.db.bustedX
sqlite3 packages.data.db < backup
rm backup

Essentially, even though the DB reports as corrupt. The SQLite tool can dump it and then recreate it.

Cheers!