Right now, running locally, every action from the Meteor CLI in OSX throws this exception:
/Users/mallorym/.meteor/packages/meteor-tool/.1.1.3.1d614zp
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!