Using latest plexus-compiler-eclipse (and ecj), when changing a java file and just compiling without clean, I'm getting:

Compilation failure
Unknown source: java.lang.IllegalArgumentException: File /home/foo/target/generated-sources/annotations/foo/SomeMapperImpl.java is specified more than once

The mapper is generated via mapstruct.

When adding -X I can see here that the file is indeed passed twice to ECJ:
https://github.com/codehaus-plexus/plexus-compiler/blob/plexus-compiler-2.12.0/plexus-compilers/plexus-compiler-eclipse/src/main/java/org/codehaus/plexus/compiler/eclipse/EclipseJavaCompiler.java#L357

Cause:

• file is added initially here (as expected): https://github.com/codehaus-plexus/plexus-compiler/blob/plexus-compiler-2.12.0/plexus-compilers/plexus-compiler-eclipse/src/main/java/org/codehaus/plexus/compiler/eclipse/EclipseJavaCompiler.java#L247
• but it is added again via addExtraSources():

  plexus-compiler/plexus-compilers/plexus-compiler-eclipse/src/main/java/org/codehaus/plexus/compiler/eclipse/EclipseJavaCompiler.java

  Lines 628 to 638 in f6c899b

  	private void addExtraSources( File dir, List<String> allSources )
  	{
  	DirectoryScanner scanner = new DirectoryScanner();
  	scanner.setBasedir( dir.getAbsolutePath() );
  	scanner.setIncludes( new String[]{ "**/*.java" } );
  	scanner.scan();
  	for ( String file : scanner.getIncludedFiles() )
  	{
  	allSources.add( new File( dir, file ).getAbsolutePath() );
  	}
  	}

Potential fix: use Set or make addExtraSources() more intelligent.