I had a similar problem, but I did not want to move the resources to src / test / resources for various reasons. However, I could solve the problem by explicitly adding all the subfolders to pom.xml, as shown in the following snippet:
<build>
<resources>
<resource>
<directory>myFolder/subFolder1</directory>
</resource>
<resource>
<directory>myFolder/subFolder2</directory>
</resource>
<resource>
<directory>myFolder/subFolder3</directory>
</resource>
</resources>
[....]
</build>
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