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PhpStorm provides database prefixes support and changes #__  on fly to the prefix that is defined in the $dbprefix field in the configuration.php file (. You will also have completion working for your SQL queries.To have it working make sure that SQL Dialect for project is equal to Database (Settings-> SQL Dialects)

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If you click Ctrl+Click you can navigate directly to the table from the query.

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Joomla! Doc-blocks standard support

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