[Bug]: Duplicate classes when trying to compile in IntelliJ

[adamretter]

Describe the bug

If you use the spoon-maven-plugin in your project, it then seems that you can no longer compile the project in IntelliJ as you get errors about java: duplicate class: MyClass for every class that is processed by spoon.

I believe that this is because src/main/java contains a copy of the class (.java) file, and then also target/generated-sources/spoon contains another (processed) copy of the class (.java) file.

IntelliJ doesn't seem to understand that the original copy in src/main/java should be ignored, and there seems to be no easy way to configure this (e.g. remove src/main/java as a source root) without breaking many things.

NOTE - the build still works fine outside of IntelliJ when using mvn from the CLI; but IntelliJ is probably the most popular IDE, and we need to use it here.

Any ideas?

Source code you are trying to analyze/transform

Example Maven plugin config from pom.xml:

<plugin>
    <groupId>fr.inria.gforge.spoon</groupId>
    <artifactId>spoon-maven-plugin</artifactId>
    <version>3.8.0</version>
    <executions>
        <execution>
            <id>spoonify</id>
            <phase>generate-sources</phase>
            <goals>
                <goal>generate</goal>
            </goals>
            <configuration>
                <compliance>21</compliance>
                <noCopyResources>true</noCopyResources>
                <processors>
                    <processor>xyz.elemental.build.tools.spoon.processors.PermissionRequiredProcessor</processor>
                </processors>
            </configuration>
        </execution>
    </executions>
    <dependencies>
        <dependency>
            <groupId>fr.inria.gforge.spoon</groupId>
            <artifactId>spoon-core</artifactId>
            <version>11.2.1</version>
        </dependency>
        <dependency>
            <groupId>xyz.elemental</groupId>
            <artifactId>exist-core-build-tools</artifactId>
            <version>${project.version}</version>
        </dependency>
    </dependencies>
</plugin>

Spoon Version

spoon: 11.8.2
spoon-maven-plugin: 3.8.0
IntelliJ: 2025.2.1

JVM Version

21

What operating system are you using?

macOS

[monperrus]

Thanks for the bug report.

One option would be to configure spoon-maven-plugin to only output new classes.

Reading the docs, skipGeneratedSources might be a first step in this direction.

Looking forward to hearing about your progress!