Under android studio 3.0 & gradle 4.1 milestone, I encountered the compile error:

Caused by: java.lang.RuntimeException: Unexpected scopes found in folder '/app/build/intermediates/transforms/AspectTransform/debug'. Required: PROJECT, SUB_PROJECTS, EXTERNAL_LIBRARIES. Found: EXTERNAL_LIBRARIES, PROJECT, PROJECT_LOCAL_DEPS, SUB_PROJECTS, SUB_PROJECTS_LOCAL_DEPS at com.android.build.gradle.internal.pipeline.IntermediateFolderUtils.makeRestrictedCopies(IntermediateFolderUtils.java:455) at com.android.build.gradle.internal.pipeline.IntermediateFolderUtils.<init>(IntermediateFolderUtils.java:66) at com.android.build.gradle.internal.pipeline.IntermediateStream.init(IntermediateStream.java:191) at com.android.build.gradle.internal.pipeline.IntermediateStream.asNonIncrementalInput(IntermediateStream.java:146) at com.android.build.gradle.internal.pipeline.TransformTask.computeNonIncTransformInput(TransformTask.java:281) at com.android.build.gradle.internal.pipeline.TransformTask.access$500(TransformTask.java:70) at com.android.build.gradle.internal.pipeline.TransformTask$1.call(TransformTask.java:196) at com.android.build.gradle.internal.pipeline.TransformTask$1.call(TransformTask.java:157) at com.android.builder.profile.ThreadRecorder.record(ThreadRecorder.java:102) at com.android.build.gradle.internal.pipeline.TransformTask.transform(TransformTask.java:152) at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:168) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:134) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:121) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)

I checked the build output dir, and there is a exactly a AspectTransform directory. maybe gradle considers it invalid?

I'm also working with hugo, and knows that our plugin works the same as hugo in the AspectJ part, so i made a compartion of source code between them.

the Hugo plugin is as follows:
JavaCompile javaCompile = variant.javaCompile javaCompile.doLast { String[] args = [ "-showWeaveInfo", "-1.5", "-inpath", javaCompile.destinationDir.toString(), "-aspectpath", javaCompile.classpath.asPath, "-d", javaCompile.destinationDir.toString(), "-classpath", javaCompile.classpath.asPath, "-bootclasspath", project.android.bootClasspath.join(File.pathSeparator) ] log.debug "ajc args: " + Arrays.toString(args) ......
and our plugin:
`def args = [
"-showWeaveInfo",
"-encoding", encoding,
"-source", sourceCompatibility,
"-target", targetCompatibility,
"-d", destinationDir,
"-classpath", classPath.join(File.pathSeparator),
"-bootclasspath", bootClassPath
]

    if (!getInPath().isEmpty()) {
        args << '-inpath'
        args << getInPath().join(File.pathSeparator)
    }
    if (!getAspectPath().isEmpty()) {
        args << '-aspectpath'
        args << getAspectPath().join(File.pathSeparator)
    }`

i doubt that the output dir differs, which caused gradle report this exception.