SpringBoot CDS extract fails if application has its own META-INF directory

Tried using the new -Djarmode=tools mode with Spring Boot 3.3.0 on my application and the extraction failed (stack trace below). It turns out to be because my application has a META-INF directory with a service configuration. If I remove my src/main/resources/META-INF directory and build the fat jar again, the extraction succeeds.

Repo: https://github.com/terraware/terraware-server

What I ran:

./gradlew bootJar
cd build/libs
java -Djarmode=tools -jar terraware-server-*.jar extract

Stack trace:

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:118)
    at java.base/java.lang.reflect.Method.invoke(Method.java:580)
    at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:91)
    at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:53)
    at org.springframework.boot.loader.launch.JarLauncher.main(JarLauncher.java:58)
Caused by: java.lang.IllegalStateException: java.io.UncheckedIOException: java.util.zip.ZipException: duplicate entry: META-INF/services/
    at org.springframework.boot.jarmode.tools.ToolsJarMode.run(ToolsJarMode.java:56)
    at org.springframework.boot.loader.launch.JarModeRunner.main(JarModeRunner.java:43)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
    ... 4 more
Caused by: java.io.UncheckedIOException: java.util.zip.ZipException: duplicate entry: META-INF/services/
    at org.springframework.boot.jarmode.tools.ExtractCommand.run(ExtractCommand.java:118)
    at org.springframework.boot.jarmode.tools.Command.run(Command.java:112)
    at org.springframework.boot.jarmode.tools.Runner.runCommand(Runner.java:68)
    at org.springframework.boot.jarmode.tools.Runner.run(Runner.java:55)
    at org.springframework.boot.jarmode.tools.Runner.run(Runner.java:47)
    at org.springframework.boot.jarmode.tools.ToolsJarMode.run(ToolsJarMode.java:53)
    ... 6 more
Caused by: java.util.zip.ZipException: duplicate entry: META-INF/services/
    at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:259)
    at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:115)
    at org.springframework.boot.jarmode.tools.ExtractCommand.lambda$createApplication$3(ExtractCommand.java:258)
    at org.springframework.boot.jarmode.tools.ExtractCommand.withJarEntries(ExtractCommand.java:333)
    at org.springframework.boot.jarmode.tools.ExtractCommand.createApplication(ExtractCommand.java:254)
    at org.springframework.boot.jarmode.tools.ExtractCommand.run(ExtractCommand.java:114)
    ... 11 more

Relevant contents of jarfile (unzip -l terraware-server-*.jar | grep META-INF):

        0  05-29-2024 17:29   META-INF/
      441  05-29-2024 17:29   META-INF/MANIFEST.MF
        0  02-01-1980 00:00   META-INF/services/
       66  02-01-1980 00:00   META-INF/services/java.nio.file.spi.FileSystemProvider
        0  05-29-2024 17:29   BOOT-INF/classes/META-INF/
     2884  05-29-2024 17:29   BOOT-INF/classes/META-INF/terraware-server.kotlin_module
        0  05-29-2024 17:29   BOOT-INF/classes/META-INF/services/
       70  05-29-2024 17:29   BOOT-INF/classes/META-INF/services/java.text.spi.DecimalFormatSymbolsProvider
        0  05-29-2024 10:29   META-INF/BOOT.SF

Comment From: scottfrederick

Duplicates #40903. Can you try with the latest 3.3.1-SNAPSHOT build?

Comment From: sgrimm

Ah, thanks, overlooked that issue because I wasn't doing an AOT build. Can confirm that the problem is fixed in 3.3.1-SNAPSHOT.

Comment From: wilkinsona

I've updated the title of #40903 to reflect the broader nature of the problem.