Kapt, Maven: Fix running with the non-clean build (KT-20816)

Clean target directories for kapt stubs and generated source files.
Filter out the compile destination directory from the classpath.

libraries/tools/kotlin-maven-plugin/src/main/java/org/jetbrains/kotlin/maven/K2JVMCompileMojo.java

@@ -132,6 +132,10 @@ public class K2JVMCompileMojo extends KotlinCompileMojoBase<K2JVMCompilerArgumen
         return paths;
     }
 
+    protected List<String> getClasspath() {
+        return filterClassPath(project.getBasedir(), classpath);
+    }
+
     @NotNull
     protected String getSourceSetName() {
         return AnnotationProcessingManager.COMPILE_SOURCE_SET_NAME;
@@ -150,7 +154,7 @@ public class K2JVMCompileMojo extends KotlinCompileMojoBase<K2JVMCompilerArgumen
             getLog().warn("Parameters module and testModule are deprecated and ignored, they will be removed in further release.");
         }
 
-        List<String> classpathList = filterClassPath(project.getBasedir(), classpath);
+        List<String> classpathList = getClasspath();
 
         if (!classpathList.isEmpty()) {
             String classPathString = join(classpathList, File.pathSeparator);

libraries/tools/kotlin-maven-plugin/src/main/java/org/jetbrains/kotlin/maven/kapt/KaptJVMCompilerMojo.java

@@ -33,6 +33,7 @@ import org.jetbrains.kotlin.maven.K2JVMCompileMojo;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.jetbrains.kotlin.maven.Util.joinArrays;
 import static org.jetbrains.kotlin.maven.kapt.AnnotationProcessingManager.*;
@@ -129,6 +130,28 @@ public class KaptJVMCompilerMojo extends K2JVMCompileMojo {
         return super.execCompiler(compiler, messageCollector, arguments, sourceRoots);
     }
 
+    @Override
+    protected List<String> getSourceFilePaths() {
+        File generatedSourcesDirectory = getGeneratedSourcesDirectory(project, getSourceSetName());
+
+        return super.getSourceFilePaths()
+                .stream()
+                .filter(path -> !new File(path).equals(generatedSourcesDirectory))
+                .collect(Collectors.toList());
+    }
+
+    @Override
+    protected List<String> getClasspath() {
+        File compileTargetDirectory = new File(this.output);
+
+        // TODO it seems for me that the target directory should not be in the compile classpath
+        // We filter out it here, but it's definitely a work-around.
+        return super.getClasspath()
+                .stream()
+                .filter(path -> !new File(path).equals(compileTargetDirectory))
+                .collect(Collectors.toList());
+    }
+
     protected void addKaptSourcesDirectory(@NotNull String path) {
         project.addCompileSourceRoot(path);
     }