Unfortunately, we don't have any automatic drop-table feature, but
I agree it would be handy (you might want to make a JIRA report
with the suggestion).
Note that the "SynchronizeMappings" property allows you to use all
the arguments of the mappingtool. So you can try something like:
buildSchema(SchemaAction=refresh, DropTables=true)
Theoretically, that will drop unused columns and tables while adding
any new columns and tables needed for your mappings. If you try it,
let us know how it works out.
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