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The NetBeans project system recognizes sql files and even allows you to double-click a sql file to open it in the SQL editor. However, the SQL Editor fails to execute that file. Note, according to the NetBeans help documentation, this is possible: "You can use the SQL Editor to create, edit and execute any SQL files in your project. To open an SQL file, right-click the SQL file ( ) in the Projects or Files window and choose Open. You can also double-click the icon to open the file in the SQL Editor."
This is as designed for 5.0, although the help is a little bit misleading. The execution of scripts consisting of multiple statements is planned for the next version: http://db.netbeans.org/uispecs/sqleditor/sqleditor-ui-spec-promo-g.html
*** Issue 18475 has been marked as a duplicate of this issue. ***
Implemented in the release55 branch.