Fixed collecting source files for multiple modules in incremental compilation.

Error led to analyzing same file twice.

jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilder.java

@@ -22,6 +22,7 @@ import com.intellij.openapi.util.io.StreamUtil;
 import com.intellij.openapi.util.text.StringUtil;
 import com.intellij.util.Function;
 import com.intellij.util.containers.ContainerUtil;
+import com.intellij.util.containers.MultiMap;
 import gnu.trove.THashSet;
 import kotlin.Pair;
 import org.jetbrains.annotations.NotNull;
@@ -180,9 +181,11 @@ public class KotlinBuilder extends ModuleLevelBuilder {
                         NO_LOCATION);
             }
 
-            List<File> filesToCompile = KotlinSourceFileCollector.getDirtySourceFiles(dirtyFilesHolder);
+            MultiMap<ModuleBuildTarget, File> filesToCompile = KotlinSourceFileCollector.getDirtySourceFiles(dirtyFilesHolder);
-            filesToCompile.removeAll(allCompiledFiles);
+            for (ModuleBuildTarget target : filesToCompile.keySet()) {
-            allCompiledFiles.addAll(filesToCompile);
+                filesToCompile.getModifiable(target).removeAll(allCompiledFiles);
+            }
+            allCompiledFiles.addAll(filesToCompile.values());
 
             Set<ModuleBuildTarget> processedTargetsWithRemoved = getProcessedTargetsWithRemovedFilesContainer(context);
 

jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilderModuleScriptGenerator.java

@@ -19,6 +19,7 @@ package org.jetbrains.jet.jps.build;
 import com.intellij.openapi.util.io.FileUtil;
 import com.intellij.openapi.util.text.StringUtil;
 import com.intellij.util.containers.ContainerUtil;
+import com.intellij.util.containers.MultiMap;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jet.compiler.runner.KotlinModuleDescriptionBuilder;
@@ -56,7 +57,7 @@ public class KotlinBuilderModuleScriptGenerator {
     public static File generateModuleDescription(
             CompileContext context,
             ModuleChunk chunk,
-            List<File> sourceFiles, // ignored for non-incremental compilation
+            MultiMap<ModuleBuildTarget, File> sourceFiles, // ignored for non-incremental compilation
             boolean hasRemovedFiles
     )
             throws IOException
@@ -73,15 +74,16 @@ public class KotlinBuilderModuleScriptGenerator {
         for (ModuleBuildTarget target : chunk.getTargets()) {
             File outputDir = getOutputDir(target);
 
-            if (!IncrementalCompilation.ENABLED) {
+            List<File> moduleSources = new ArrayList<File>(
-                sourceFiles = new ArrayList<File>(KotlinSourceFileCollector.getAllKotlinSourceFiles(target));
+                    IncrementalCompilation.ENABLED
-            }
+                    ? sourceFiles.get(target)
+                    : KotlinSourceFileCollector.getAllKotlinSourceFiles(target));
 
             if (sourceFiles.size() > 0 || hasRemovedFiles) {
                 noSources = false;
 
                 if (logger.isEnabled()) {
-                    logger.logCompiledFiles(sourceFiles, KotlinBuilder.KOTLIN_BUILDER_NAME, "Compiling files:");
+                    logger.logCompiledFiles(moduleSources, KotlinBuilder.KOTLIN_BUILDER_NAME, "Compiling files:");
                 }
             }
 
@@ -89,7 +91,7 @@ public class KotlinBuilderModuleScriptGenerator {
                     target.getId(),
                     outputDir.getAbsolutePath(),
                     getKotlinModuleDependencies(context, target),
-                    sourceFiles,
+                    moduleSources,
                     target.isTests(),
                     // this excludes the output directories from the class path, to be removed for true incremental compilation
                     outputDirs

jps-plugin/src/org/jetbrains/jet/jps/build/KotlinSourceFileCollector.java

@@ -22,6 +22,7 @@ import com.intellij.openapi.util.io.FileUtilRt;
 import com.intellij.util.Function;
 import com.intellij.util.Processor;
 import com.intellij.util.containers.ContainerUtil;
+import com.intellij.util.containers.MultiMap;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.jps.builders.DirtyFilesHolder;
 import org.jetbrains.jps.builders.FileProcessor;
@@ -39,21 +40,21 @@ import java.util.List;
 
 public class KotlinSourceFileCollector {
     // For incremental compilation
-    public static List<File> getDirtySourceFiles(DirtyFilesHolder<JavaSourceRootDescriptor, ModuleBuildTarget> dirtyFilesHolder)
+    public static MultiMap<ModuleBuildTarget, File> getDirtySourceFiles(DirtyFilesHolder<JavaSourceRootDescriptor, ModuleBuildTarget> dirtyFilesHolder)
             throws IOException
     {
-        final List<File> sourceFiles = ContainerUtil.newArrayList();
+        final MultiMap<ModuleBuildTarget, File> result = new MultiMap<ModuleBuildTarget, File>();
 
         dirtyFilesHolder.processDirtyFiles(new FileProcessor<JavaSourceRootDescriptor, ModuleBuildTarget>() {
             @Override
             public boolean apply(ModuleBuildTarget target, File file, JavaSourceRootDescriptor root) throws IOException {
                 if (isKotlinSourceFile(file)) {
-                    sourceFiles.add(file);
+                    result.putValue(target, file);
                 }
                 return true;
             }
         });
-        return sourceFiles;
+        return result;
     }
 
     @NotNull