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Yes, my issue same your question. I set $config['migration_auto_latest'] = TRUE; and run php cli migrate not update version lasted.
And how to update table using cli migration? Example: I created User table migration and now I want alter column table or add new column into User table.
When your config/migrations.php has the following:
$config['migration_auto_latest'] = TRUE;
The command 'php cli migrate' still does not perform the migrations unless the version number is set.
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