duplicate file if try to build with another snakeyaml deps

[lfarkas]

if someone try to build it with anything that already use snakeyaml (eg. quarkus) than duplicate warning will be got during build:

Dependencies with duplicate files detected. The dependencies [org.yaml:snakeyaml::jar:2.0[paths: /home/lfarkas/.gradle/caches/modules-2/files-2.1/org.yaml/snakeyaml/2.0/3aab2116756442bf0d4cd1c089b24d34c3baa253/snakeyaml-2.0.jar;], io.prometheus.jmx:jmx_prometheus_javaagent::jar:0.18.0[paths: /home/lfarkas/.gradle/caches/modules-2/files-2.1/io.prometheus.jmx/jmx_prometheus_javaagent/0.18.0/889ad8ac7b516a751b50a2a7ce82f611d34f8376/jmx_prometheus_javaagent-0.18.0.jar;]] contain duplicate files, e.g. META-INF/versions/9/org/yaml/snakeyaml/internal/Logger$Level.class

the bigger problem happened during execution of such projects since it produce this error:

Exception in thread "main" java.lang.NoClassDefFoundError: io/prometheus/jmx/shaded/org/yaml/snakeyaml/internal/Logger (wrong name: org/yaml/snakeyaml/internal/Logger)
	at java.base/java.lang.ClassLoader.defineClass1(Native Method)
	at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1012)
	at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:150)
	at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:862)
	at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:760)
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:681)
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:639)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
	at org.yaml.snakeyaml.TypeDescription.<clinit>(TypeDescription.java:43)
	at org.yaml.snakeyaml.constructor.Constructor.<init>(Constructor.java:60)
	at org.yaml.snakeyaml.constructor.Constructor.<init>(Constructor.java:50)
	at org.yaml.snakeyaml.Yaml.<init>(Yaml.java:73)
	at io.smallrye.config.source.yaml.YamlConfigSource.<clinit>(YamlConfigSource.java:47)
	at io.quarkus.config.yaml.runtime.ApplicationYamlConfigSourceLoader.loadConfigSource(ApplicationYamlConfigSourceLoader.java:27)
	at io.smallrye.config.AbstractLocationConfigSourceLoader.addConfigSource(AbstractLocationConfigSourceLoader.java:236)
	at io.smallrye.config.AbstractLocationConfigSourceLoader.addConfigSource(AbstractLocationConfigSourceLoader.java:231)
	at io.smallrye.config.AbstractLocationConfigSourceLoader$ConfigSourcePathConsumer.accept(AbstractLocationConfigSourceLoader.java:329)
	at io.smallrye.config.AbstractLocationConfigSourceLoader$ConfigSourcePathConsumer.accept(AbstractLocationConfigSourceLoader.java:316)
	at io.smallrye.common.classloader.ClassPathUtils.lambda$consumeAsPath$0(ClassPathUtils.java:103)
	at io.smallrye.common.classloader.ClassPathUtils.processAsPath(ClassPathUtils.java:144)
	at io.smallrye.common.classloader.ClassPathUtils.consumeAsPath(ClassPathUtils.java:102)
	at io.smallrye.common.classloader.ClassPathUtils.consumeAsPaths(ClassPathUtils.java:86)
	at io.smallrye.config.AbstractLocationConfigSourceLoader.tryClassPath(AbstractLocationConfigSourceLoader.java:139)
	at io.smallrye.config.AbstractLocationConfigSourceLoader.loadConfigSources(AbstractLocationConfigSourceLoader.java:102)
	at io.smallrye.config.AbstractLocationConfigSourceLoader.loadConfigSources(AbstractLocationConfigSourceLoader.java:85)
	at io.quarkus.config.yaml.runtime.ApplicationYamlConfigSourceLoader$InClassPath.getConfigSources(ApplicationYamlConfigSourceLoader.java:35)
	at io.quarkus.config.yaml.runtime.ApplicationYamlConfigSourceLoader$InClassPath.getConfigSources(ApplicationYamlConfigSourceLoader.java:30)
	at io.smallrye.config.SmallRyeConfig$ConfigSources.buildSources(SmallRyeConfig.java:581)
	at io.smallrye.config.SmallRyeConfig$ConfigSources.<init>(SmallRyeConfig.java:537)
	at io.smallrye.config.SmallRyeConfig.<init>(SmallRyeConfig.java:69)
	at io.smallrye.config.SmallRyeConfigBuilder.build(SmallRyeConfigBuilder.java:623)
	at io.quarkus.runtime.generated.Config.<clinit>(Unknown Source)
	at io.quarkus.runner.ApplicationImpl.<clinit>(Unknown Source)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
	at io.quarkus.runtime.Quarkus.run(Quarkus.java:70)
	at io.quarkus.runtime.Quarkus.run(Quarkus.java:44)

[dhoard]

This appears to be related to https://issues.apache.org/jira/browse/MSHADE-439

The maven-shade-plugin declaration for jmx_prometheus_javaagent can be changed to filter the classes. This should resolve the issue, but it's not clear on the overall impact on other applications.

<filters>
    <filter>
        <artifact>org.yaml:snakeyaml</artifact>
        <excludes>
            <exclude>META-INF/versions/9/org/yaml/snakeyaml/internal/**</exclude>
        </excludes>
    </filter>
</filters>

I'll have to do some more research/integration testing.

[dhoard]

@lfarkas Can you create a simple GitHub project that I can clone and reproduce the issue?