Also show executed SQL code for addAtomToConcept

Kind of dirty: emitLog is in Database.php. Would be better to keep logging in a separate module.
Remove old commented (and incorrect) case
Temporary commit, which seems to fix the issue.

Adding the concept beforehand makes the old case of update usable. Need to check if this always works. The old comment seems to suggest it doesn't, but that might be a mistake.