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I am using IntelliJ IDEA 11.1.2 Ultimate with Gradle 1.0 multi module project. One module represents the domain. 
The projects output is points to [project-root]\out. But if I run a unit test the output folder of the domain module does not contain any .sql files at all. 
. This is how I run the JUnit test within IntelliJ IDEA 
.
If I run the project using Gradle from command line everything works fine.
Settings|Compiler|Resource Patterns, add the pattern for thesqlextension.