java.lang.LinkageError from quarkus:dev, using entities from external jars

[tgippi]

Describe the bug
Quarkus startup with mvn quarkus:dev fails with java.lang.LinkageError, as soon as we use quarkus.index-dependency for external dependencies which contain javax.persistence annotated classes (e.g. JPA Entities).
It doesn't happen when we run the packaged jar file directly by using java -jar target/getting-started-1.0-SNAPSHOT-runner.jar

Expected behavior
Startup with mvn quarkus:dev should not fail with java.lang.LinkageError

Actual behavior
Quarkus fails to start when we use mvn quarkus:dev, complaining about java.lang.LinkageError.

To Reproduce
Steps to reproduce the behavior:

1. git clone [email protected]:tgippi/quarkus-issue.git
2. mvn quarkus:dev

Configuration

quarkus.datasource.url=jdbc:h2:mem:test
quarkus.datasource.driver=org.h2.Driver

quarkus.index-dependency.axon-messaging.group-id=org.axonframework
quarkus.index-dependency.axon-messaging.artifact-id=axon-messaging
quarkus.index-dependency.axon-eventsourcing.group-id=org.axonframework
quarkus.index-dependency.axon-eventsourcing.artifact-id=axon-eventsourcing
quarkus.index-dependency.axon-configuration.group-id=org.axonframework
quarkus.index-dependency.axon-configuration.artifact-id=axon-configuration

Screenshots

2020-02-03 20:42:53,467 ERROR [io.qua.application] (main) Failed to start application: java.lang.LinkageError: loader constraint violation: loader 'app' wants to load interface org.axonframework.common.jpa.EntityManagerProvider. A different interface with the same name was previously loaded by io.quarkus.runner.RuntimeClassLoader @15b3e5b. (org.axonframework.common.jpa.EntityManagerProvider is in unnamed module of loader io.quarkus.runner.RuntimeClassLoader @15b3e5b, parent loader java.net.URLClassLoader @548ad73b)
        at java.base/java.lang.ClassLoader.defineClass1(Native Method)
        at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
        at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
        at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
        at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
        at org.axonframework.config.AggregateConfigurer.jpaMappedConfiguration(AggregateConfigurer.java:183)
        at org.acme.quickstart.AxonStarter.startup(AxonStarter.java:28)
        at org.acme.quickstart.AxonStarter_Observer_startup_f43ab41051de39ca1e534f6cd06115c3c9b219b8.notify(AxonStarter_Observer_startup_f43ab41051de39ca1e534f6cd06115c3c9b219b8.zig:111)
        at io.quarkus.arc.impl.EventImpl$Notifier.notifyObservers(EventImpl.java:282)
        at io.quarkus.arc.impl.EventImpl$Notifier.notify(EventImpl.java:267)
        at io.quarkus.arc.impl.EventImpl.fire(EventImpl.java:69)
        at io.quarkus.arc.runtime.LifecycleEventRunner.fireStartupEvent(LifecycleEventRunner.java:23)
        at io.quarkus.arc.runtime.ArcRecorder.handleLifecycleEvents(ArcRecorder.java:108)
        at io.quarkus.deployment.steps.LifecycleEventsBuildStep$startupEvent36.deploy_0(LifecycleEventsBuildStep$startupEvent36.zig:58)
        at io.quarkus.deployment.steps.LifecycleEventsBuildStep$startupEvent36.deploy(LifecycleEventsBuildStep$startupEvent36.zig:77)
        at io.quarkus.runner.ApplicationImpl.doStart(ApplicationImpl.zig:185)
        at io.quarkus.runtime.Application.start(Application.java:87)
        at io.quarkus.runner.RuntimeRunner.run(RuntimeRunner.java:167)
        at io.quarkus.dev.DevModeMain.doStart(DevModeMain.java:178)
        at io.quarkus.dev.DevModeMain.start(DevModeMain.java:96)
        at io.quarkus.dev.DevModeMain.main(DevModeMain.java:67)

2020-02-03 20:42:53,476 ERROR [io.qua.dev.DevModeMain] (main) Failed to start Quarkus: java.lang.RuntimeException: Failed to start quarkus
        at io.quarkus.runner.ApplicationImpl.doStart(ApplicationImpl.zig:215)
        at io.quarkus.runtime.Application.start(Application.java:87)
        at io.quarkus.runner.RuntimeRunner.run(RuntimeRunner.java:167)
        at io.quarkus.dev.DevModeMain.doStart(DevModeMain.java:178)
        at io.quarkus.dev.DevModeMain.start(DevModeMain.java:96)
        at io.quarkus.dev.DevModeMain.main(DevModeMain.java:67)
Caused by: java.lang.LinkageError: loader constraint violation: loader 'app' wants to load interface org.axonframework.common.jpa.EntityManagerProvider. A different interface with the same name was previously loaded by io.quarkus.runner.RuntimeClassLoader @15b3e5b. (org.axonframework.common.jpa.EntityManagerProvider is in unnamed module of loader io.quarkus.runner.RuntimeClassLoader @15b3e5b, parent loader java.net.URLClassLoader @548ad73b)
        at java.base/java.lang.ClassLoader.defineClass1(Native Method)
        at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
        at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
        at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
        at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
        at org.axonframework.config.AggregateConfigurer.jpaMappedConfiguration(AggregateConfigurer.java:183)
        at org.acme.quickstart.AxonStarter.startup(AxonStarter.java:28)
        at org.acme.quickstart.AxonStarter_Observer_startup_f43ab41051de39ca1e534f6cd06115c3c9b219b8.notify(AxonStarter_Observer_startup_f43ab41051de39ca1e534f6cd06115c3c9b219b8.zig:111)
        at io.quarkus.arc.impl.EventImpl$Notifier.notifyObservers(EventImpl.java:282)
        at io.quarkus.arc.impl.EventImpl$Notifier.notify(EventImpl.java:267)
        at io.quarkus.arc.impl.EventImpl.fire(EventImpl.java:69)
        at io.quarkus.arc.runtime.LifecycleEventRunner.fireStartupEvent(LifecycleEventRunner.java:23)
        at io.quarkus.arc.runtime.ArcRecorder.handleLifecycleEvents(ArcRecorder.java:108)
        at io.quarkus.deployment.steps.LifecycleEventsBuildStep$startupEvent36.deploy_0(LifecycleEventsBuildStep$startupEvent36.zig:58)
        at io.quarkus.deployment.steps.LifecycleEventsBuildStep$startupEvent36.deploy(LifecycleEventsBuildStep$startupEvent36.zig:77)
        at io.quarkus.runner.ApplicationImpl.doStart(ApplicationImpl.zig:185)
        ... 5 more

Environment (please complete the following information):

• Output of uname -a or ver: Linux tobi-Z97-HD3 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
• Output of java -version: openjdk version "11.0.6" 2020-01-14 OpenJDK Runtime Environment (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1) OpenJDK 64-Bit Server VM (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1, mixed mode, sharing)
• GraalVM version (if different from Java): None
• Quarkus version or git rev: 1.2.0.Final

Additional context
Not sure if it is exactly the same issue #5354, so I opened a new one.
However, using the latest version 1.2.0.Final won't fix it for the reproducer project in #5354.

[tgippi]

I've just tested it on the 1.3 branch. It seems the issue has been fixed there (I guess #6411 has fixed it?)

[stuartwdouglas]

This was a known problem that should be fixed by the classloader change (I think it is a duplicate of #5354)