Error using _refresh.sh script with 3.8.0

Describe the bug
When running the _refresh.sh script in an implementation guide, I get this error:

[main] INFO org.opencds.cqf.tooling.packaging.r4.PackageMeasure - Packaging Measure IMMZIND05...
[main] WARN org.opencds.cqf.tooling.utilities.IOUtils - Unable to initialize directory at /home/publisher/ig/bundles/measure/IMMZIND05
[main] WARN org.opencds.cqf.tooling.utilities.IOUtils - Unable to initialize directory at /home/publisher/ig/bundles/measure/IMMZIND05/IMMZIND05-files
[main] INFO org.opencds.cqf.tooling.packaging.r4.PackageMeasure - Packaging Dependencies...
[main] INFO org.opencds.cqf.tooling.packaging.r4.PackageMeasure - Packaging Terminology...
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:115)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)
Caused by: java.lang.NullPointerException: Cannot invoke "String.getBytes(java.nio.charset.Charset)" because "cql" is null
at org.opencds.cqf.tooling.utilities.IOUtils.writeCqlToFile(IOUtils.java:202)
at org.opencds.cqf.tooling.packaging.r4.PackageMeasure.output(PackageMeasure.java:139)
at org.opencds.cqf.tooling.packaging.Package.packageArtifact(Package.java:75)
at org.opencds.cqf.tooling.packaging.PackageMeasures.lambda$new$0(PackageMeasures.java:16)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.opencds.cqf.tooling.packaging.PackageMeasures.(PackageMeasures.java:14)
at org.opencds.cqf.tooling.processor.IGBundleProcessor.bundleIg(IGBundleProcessor.java:41)
at org.opencds.cqf.tooling.processor.IGProcessor.publishIG(IGProcessor.java:102)
at org.opencds.cqf.tooling.operation.RefreshIGOperation.execute(RefreshIGOperation.java:38)
at org.opencds.cqf.tooling.cli.Main.main(Main.java:322)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
... 5 more

To Reproduce
This is from: https://github.com/WorldHealthOrganization/smart-immunizations/

refresh is using -rp to process the fsh-regenerated resources.

Run sushi, then _refresh.sh

Expected behavior
No error

Desktop (please complete the following information):

• OS: Linux
• Java Version: openjdk 21.0.6 2025-01-21 LTS

Additional context
This error doesn't happen in 3.7.0, although the packaging fails there.

This error only happens the first time running it after running sushi. It works on the second run.

Reproduce the failure by running sushi and then _refresh.sh with the -rp option in the linked implementation guide. Start with IOUtils.writeCqlToFile at line 202 and PackageMeasure.output at line 139, following the stack trace. Done means the first refresh after sushi completes without the NullPointerException, while retaining the successful second-run behavior.