Native Build Tools 0.9.26's native:metadata-copy causes MojoExecutionException when executed on a multi-module Maven project

[linghengqian]

Before reporting

• This repository should be used to report issues on the Maven or Gradle plugins for GraalVM.
• Please report issues which are specific to the Spring Framework or the Micronaut framework to their specific repositories.
• Do not report issues with building your specific application, e.g errors which happen at image build time like classes initialized at build time, or missing classes as run time: those are not related to the plugins but problems with configuration. You can refer to the GraalVM native image documentation for available options and the plugins documentation for how to use them with the plugin.

Describe the bug
A clear and concise description of what the bug is.
Make sure that you have read the documentation and that you are using the latest plugin version.

• Native Build Tools 0.9.26's native:metadata-copy causes MojoExecutionException when executed on a multi-module Maven project.
• I created a minimal reproducible project containing only 2 submodules, it is at https://github.com/linghengqian/nbt-v0926-metadatacopy-test . I have attached the reproduction steps and the specific Log in it.

To Reproduce

When possible, provide a link to a repository which reproduces the issue, with instructions on how to use.
The reproducer must make use of either the Maven or Gradle plugin.

Steps to reproduce the behavior:

• Execute the following command under the new Ubuntu 22.04.3 LTS instance. ./mvnw clean test is only used to verify
  that unit tests are available.

sudo apt install unzip zip curl sed -y
curl -s "https://get.sdkman.io" | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk install java 17.0.8-graalce
sdk use java 17.0.8-graalce
sudo apt-get install build-essential libz-dev zlib1g-dev -y

git clone [email protected]:linghengqian/nbt-v0926-metadatacopy-test.git
cd ./dynamic-datasource/
./mvnw clean test
./mvnw -PgenerateMetadata -DskipNativeTests -T1C -B -e clean test native:metadata-copy

• You will find that no files are output. And an exception is thrown during the metadataCopy phase.

Please use backticks to properly format code.
If possible please attach a complete reproducer here (either as a zip file or as a link to public repository/branch).

• https://github.com/linghengqian/nbt-v0926-metadatacopy-test

Expected behavior
A clear and concise description of what you expected to happen.

• ./mvnw -PgenerateMetadata -DskipNativeTests -T1C -B -e clean test native:metadata-copy has no exception and has normal JSON file output.

Logs
Add logs to help explain your problem.
Please use backticks to properly format big logs. Example:

```
<log content> 
```

**Error Log as follow**

$ ./mvnw -PgenerateMetadata -DskipNativeTests -T1C -B -e clean test native:metadata-copy
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] Found GraalVM installation from JAVA_HOME variable.
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] nbt-v0926-metadatacopy-test                                        [pom]
[INFO] curator-client                                                     [jar]
[INFO] curator-framework                                                  [jar]
[INFO] 
[INFO] Using the MultiThreadedBuilder implementation with a thread count of 6
[INFO] 
[INFO] ---------------< com.lingh:nbt-v0926-metadatacopy-test >----------------
[INFO] Building nbt-v0926-metadatacopy-test 1.0-SNAPSHOT                  [1/3]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[WARNING] *****************************************************************
[WARNING] * Your build is requesting parallel execution, but this         *
[WARNING] * project contains the following plugin(s) that have goals not  *
[WARNING] * marked as thread-safe to support parallel execution.          *
[WARNING] * While this /may/ work fine, please look for plugin updates    *
[WARNING] * and/or request plugins be made thread-safe.                   *
[WARNING] * If reporting an issue, report it against the plugin in        *
[WARNING] * question, not against Apache Maven.                           *
[WARNING] *****************************************************************
[WARNING] The following plugins are not marked as thread-safe in nbt-v0926-metadatacopy-test:
[WARNING]   org.graalvm.buildtools:native-maven-plugin:0.9.25
[WARNING] 
[WARNING] Enable debug to see precisely which goals are not marked as thread-safe.
[WARNING] *****************************************************************
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ nbt-v0926-metadatacopy-test ---
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:merge-agent-files (test-native) @ nbt-v0926-metadatacopy-test ---
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:test (test-native) @ nbt-v0926-metadatacopy-test ---
[INFO] Skipping native-image tests (parameter 'skipTests' or 'skipNativeTests' is true).
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:metadata-copy (default-cli) @ nbt-v0926-metadatacopy-test ---
[WARNING] Destination directory /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/src/test/resources/META-INF/native-image/com.lingh/nbt-v0926-metadatacopy-test doesn't exist.
[WARNING] Creating directory at: /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/src/test/resources/META-INF/native-image/com.lingh/nbt-v0926-metadatacopy-test
[INFO] Found GraalVM installation from JAVA_HOME variable.
[WARNING] Cannot find source directory /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/target/native/agent-output/test for metadata copy. Please check if you configured agent properly and it generates all necessary directories. If you want to skipp copy from some source, please configure metadataCopy with disable stage you want to skipp.
[INFO] Metadata copy process finished.
[INFO] 
[INFO] ----------------------< com.lingh:curator-client >----------------------
[INFO] 
[INFO] Building curator-client 1.0-SNAPSHOT                               [2/3]
[INFO] --------------------< com.lingh:curator-framework >---------------------
[INFO]   from curator-client/pom.xml
[INFO] Building curator-framework 1.0-SNAPSHOT                            [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]   from curator-framework/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] *****************************************************************
[WARNING] * Your build is requesting parallel execution, but this         *
[WARNING] *****************************************************************
[WARNING] * project contains the following plugin(s) that have goals not  *
[WARNING] * Your build is requesting parallel execution, but this         *
[WARNING] * project contains the following plugin(s) that have goals not  *
[WARNING] * marked as thread-safe to support parallel execution.          *
[WARNING] * marked as thread-safe to support parallel execution.          *
[WARNING] * While this /may/ work fine, please look for plugin updates    *
[WARNING] * While this /may/ work fine, please look for plugin updates    *
[WARNING] * and/or request plugins be made thread-safe.                   *
[WARNING] * and/or request plugins be made thread-safe.                   *
[WARNING] * If reporting an issue, report it against the plugin in        *
[WARNING] * question, not against Apache Maven.                           *
[WARNING] *****************************************************************
[WARNING] The following plugins are not marked as thread-safe in curator-client:
[WARNING]   org.graalvm.buildtools:native-maven-plugin:0.9.25
[WARNING] 
[WARNING] Enable debug to see precisely which goals are not marked as thread-safe.
[WARNING] *****************************************************************
[WARNING] * If reporting an issue, report it against the plugin in        *
[WARNING] * question, not against Apache Maven.                           *
[WARNING] *****************************************************************
[WARNING] The following plugins are not marked as thread-safe in curator-framework:
[WARNING]   org.graalvm.buildtools:native-maven-plugin:0.9.25
[WARNING] 
[WARNING] Enable debug to see precisely which goals are not marked as thread-safe.
[WARNING] *****************************************************************
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ curator-framework ---
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ curator-client ---
[INFO] Deleting /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-framework/target
[INFO] Deleting /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-client/target
[INFO] 
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ curator-client ---
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ curator-framework ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-client/src/main/resources
[INFO] skip non existing resourceDirectory /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-framework/src/main/resources
[INFO] 
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ curator-framework ---
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ curator-client ---
[INFO] No sources to compile
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ curator-framework ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ curator-client ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 0 resource
[INFO] Copying 0 resource
[INFO] 
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ curator-framework ---
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ curator-client ---
[INFO] Changes detected - recompiling the module!
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-framework/target/test-classes
[INFO] Compiling 1 source file to /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-client/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.1.2:test (default-test) @ curator-client ---
[INFO] 
[INFO] --- maven-surefire-plugin:3.1.2:test (default-test) @ curator-framework ---
[INFO] Surefire report directory: /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-framework/target/surefire-reports
[INFO] Surefire report directory: /home/linghengqian/TwinklingLiftWorks/git/public/nbt-v0926-metadatacopy-test/curator-client/target/surefire-reports
[INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[INFO] 
[INFO] -------------------------------------------------------
[INFO] 
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running com.lingh.CuratorFrameworkTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Running com.lingh.CuratorClientTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
SLF4J: Failed to load class "org.slf4j.impl.StaticMDCBinder".
SLF4J: Defaulting to no-operation MDCAdapter implementation.
SLF4J: See http://www.slf4j.org/codes.html#no_static_mdc_binder for further details.
SLF4J: Failed to load class "org.slf4j.impl.StaticMDCBinder".
SLF4J: Defaulting to no-operation MDCAdapter implementation.
SLF4J: See http://www.slf4j.org/codes.html#no_static_mdc_binder for further details.
/testFirst/path - CREATE
/testSecond/path - SET_DATA
/testThird/testSagittarius/path - DELETE
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.868 s -- in com.lingh.CuratorFrameworkTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:merge-agent-files (test-native) @ curator-framework ---
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:test (test-native) @ curator-framework ---
[INFO] Skipping native-image tests (parameter 'skipTests' or 'skipNativeTests' is true).
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:metadata-copy (default-cli) @ curator-framework ---
[INFO] Copying files from: test
[ERROR] Metadata copy process failed with code: 1
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.159 s -- in com.lingh.CuratorClientTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:merge-agent-files (test-native) @ curator-client ---
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:test (test-native) @ curator-client ---
[INFO] Skipping native-image tests (parameter 'skipTests' or 'skipNativeTests' is true).
[INFO] 
[INFO] --- native-maven-plugin:0.9.25:metadata-copy (default-cli) @ curator-client ---
[INFO] Copying files from: test
[ERROR] Metadata copy process failed with code: 1
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for nbt-v0926-metadatacopy-test 1.0-SNAPSHOT:
[INFO] 
[INFO] nbt-v0926-metadatacopy-test ........................ SUCCESS [  0.406 s]
[INFO] curator-client ..................................... FAILURE [  6.095 s]
[INFO] curator-framework .................................. FAILURE [  5.690 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  6.873 s (Wall Clock)
[INFO] Finished at: 2023-09-07T05:32:46+08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.graalvm.buildtools:native-maven-plugin:0.9.25:metadata-copy (default-cli) on project curator-framework: Metadata copy process failed. -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.graalvm.buildtools:native-maven-plugin:0.9.25:metadata-copy (default-cli) on project curator-framework: Metadata copy process failed.
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2 (MojoExecutor.java:375)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:351)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:171)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:163)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:210)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:195)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.Executors$RunnableAdapter.call (Executors.java:539)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1136)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:635)
    at java.lang.Thread.run (Thread.java:833)
Caused by: org.apache.maven.plugin.MojoExecutionException: Metadata copy process failed.
    at org.graalvm.buildtools.maven.MetadataCopyMojo.executeCopy (MetadataCopyMojo.java:163)
    at org.graalvm.buildtools.maven.MetadataCopyMojo.execute (MetadataCopyMojo.java:115)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2 (MojoExecutor.java:370)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:351)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:171)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:163)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:210)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:195)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.Executors$RunnableAdapter.call (Executors.java:539)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1136)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:635)
    at java.lang.Thread.run (Thread.java:833)
[ERROR] Failed to execute goal org.graalvm.buildtools:native-maven-plugin:0.9.25:metadata-copy (default-cli) on project curator-client: Metadata copy process failed. -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.graalvm.buildtools:native-maven-plugin:0.9.25:metadata-copy (default-cli) on project curator-client: Metadata copy process failed.
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2 (MojoExecutor.java:375)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:351)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:171)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:163)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:210)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:195)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.Executors$RunnableAdapter.call (Executors.java:539)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1136)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:635)
    at java.lang.Thread.run (Thread.java:833)
Caused by: org.apache.maven.plugin.MojoExecutionException: Metadata copy process failed.
    at org.graalvm.buildtools.maven.MetadataCopyMojo.executeCopy (MetadataCopyMojo.java:163)
    at org.graalvm.buildtools.maven.MetadataCopyMojo.execute (MetadataCopyMojo.java:115)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2 (MojoExecutor.java:370)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:351)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:171)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:163)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:210)
    at org.apache.maven.lifecycle.internal.builder.multithreaded.MultiThreadedBuilder$1.call (MultiThreadedBuilder.java:195)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.Executors$RunnableAdapter.call (Executors.java:539)
    at java.util.concurrent.FutureTask.run (FutureTask.java:264)
    at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1136)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:635)
    at java.lang.Thread.run (Thread.java:833)
[ERROR] 
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :curator-framework

System Info (please complete the following information):

• OS: [e.g. Windows] Ubuntu 22.04.3 LTS
• GraalVM Version [e.g. 22.0 CE] CE 17.0.8
• Java Version [e.g. 17] 17
• Plugin version [e.g. native-gradle-plugin:0.9.10] native-maven-plugin:0.9.26

Additional context
Add any other context about the problem here.

• More early investigations are at Make ShardingSphere Proxy in GraalVM Native Image form available apache/shardingsphere#21347 and Provides built-in GraalVM Reachability Metadata and submit the library information to the GRM central repo baomidou/dynamic-datasource#565 .