Provide the option to refresh the db connection
Remove error aliases when resuming population

This is important, the process will delete any index with an error
alias automatically, so we need to make sure it’s been removed. There
is a test case for this.
Fix errors in duping opts
Look up old class URIs
Pass along class objects instead of hash
Don't need ont attr
Expand hierarchy for manual annotations as well
Don't need ont attr
Cleanup var names
Move pop test setup