also extract duplicates from output folder

src/main/java/com/simpligility/maven/plugins/android/phase09package/ApkMojo.java

@@ -21,6 +21,7 @@
 import com.android.sdklib.build.DuplicateFileException;
 import com.android.sdklib.build.SealedApkException;
 import com.simpligility.maven.plugins.android.AbstractAndroidMojo;
+import com.google.common.io.Files;
 import com.simpligility.maven.plugins.android.AndroidNdk;
 import com.simpligility.maven.plugins.android.AndroidSigner;
 import com.simpligility.maven.plugins.android.IncludeExcludeSet;
@@ -51,6 +52,7 @@
 
 import java.io.File;
 import java.io.FileFilter;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.FilenameFilter;
@@ -566,7 +568,27 @@ private void computeDuplicateFiles( File jar ) throws IOException
         }
     }
 
-    private void extractDuplicateFiles( List<File> jarFiles ) throws IOException
+    private void computeDuplicateFilesInSource( File folder )
+    {
+        String rPath = folder.getAbsolutePath();
+        for ( File file : Files.fileTreeTraverser().breadthFirstTraversal( folder ).toList() )
+        {
+            String lPath = file.getAbsolutePath();
+            if ( lPath.equals( rPath ) )
+            {
+                continue; //skip the root
+            }
+            lPath = lPath.substring( rPath.length() + 1 ); //strip root folder to make relative path
+
+            if ( jars.get( lPath ) == null )
+            {
+                jars.put( lPath, new ArrayList<File>() );
+            }
+            jars.get( lPath ).add( folder );
+        }
+    }
+
+    private void extractDuplicateFiles( List<File> jarFiles, Collection<File> sourceFolders ) throws IOException
     {
         getLog().debug( "Extracting duplicates" );
         List<String> duplicates = new ArrayList<String>();
@@ -600,12 +622,20 @@ private void extractDuplicateFiles( List<File> jarFiles ) throws IOException
 
         for ( File file : jarToModify )
         {
-            final File newJar = removeDuplicatesFromJar( file, duplicates, duplicatesAdded, zos );
-            getLog().debug( "Removed duplicates from " + newJar );
-            if ( newJar != null )
+            final int index = jarFiles.indexOf( file );
+            if ( index != -1 )
             {
-                final int index = jarFiles.indexOf( file );
-                jarFiles.set( index, newJar );
+                final File newJar = removeDuplicatesFromJar( file, duplicates, duplicatesAdded, zos, index );
+                getLog().debug( "Removed duplicates from " + newJar );
+                if ( newJar != null )
+                {
+                    jarFiles.set( index, newJar );
+                }
+            }
+            else
+            {
+                removeDuplicatesFromFolder( file, file, duplicates, duplicatesAdded, zos );
+                getLog().debug( "Removed duplicates from " + file );
             }
         }
         //add transformed resources to duplicate-resources.jar
@@ -666,12 +696,17 @@ private void doAPKWithAPKBuilder( File outputFile, File dexFile, File zipArchive
             jarFiles.add( artifact.getFile() );
         }
 
+        for ( File src : sourceFolders )
+        {
+            computeDuplicateFilesInSource( src );
+        }
+
         // Check duplicates.
         if ( extractDuplicates )
         {
             try
             {
-                extractDuplicateFiles( jarFiles );
+                extractDuplicateFiles( jarFiles, sourceFolders );
             }
             catch ( IOException e )
             {
@@ -799,12 +834,14 @@ private String getNextDexFileName( int dexNumber )
     }
 
     private File removeDuplicatesFromJar( File in, List<String> duplicates,
-                                          Set<String> duplicatesAdded, ZipOutputStream duplicateZos )
+                                          Set<String> duplicatesAdded, ZipOutputStream duplicateZos, int num )
     {
         String target = targetDirectory.getAbsolutePath();
         File tmp = new File( target, "unpacked-embedded-jars" );
         tmp.mkdirs();
-        File out = new File( tmp, in.getName() );
+        String jarName = String.format( "%s-%d.%s",
+           Files.getNameWithoutExtension( in.getName() ), num, Files.getFileExtension( in.getName() ) );
+        File out = new File( tmp, jarName );
 
         if ( out.exists() )
         {
@@ -910,6 +947,66 @@ private File removeDuplicatesFromJar( File in, List<String> duplicates,
         return out;
     }
 
+    private void removeDuplicatesFromFolder( File root, File in, List<String> duplicates,
+       Set<String> duplicatesAdded, ZipOutputStream duplicateZos )
+    {
+        String rPath = root.getAbsolutePath();
+        try
+        {
+            for ( File f : in.listFiles() )
+            {
+                if ( f.isDirectory() )
+                {
+                    removeDuplicatesFromFolder( root, f, duplicates, duplicatesAdded, duplicateZos );
+                }
+                else
+                {
+                    String lName = f.getAbsolutePath();
+                    lName = lName.substring( rPath.length() + 1 ); //make relative path
+                    if ( duplicates.contains( lName ) )
+                    {
+                        boolean resourceTransformed = false;
+                        if ( transformers != null )
+                        {
+                            for ( ResourceTransformer transformer : transformers )
+                            {
+                                if ( transformer.canTransformResource( lName ) )
+                                {
+                                    getLog().info( "Transforming " + lName
+                                       + " using " + transformer.getClass().getName() );
+                                    InputStream currIn = new FileInputStream( f );
+                                    transformer.processResource( lName, currIn, null );
+                                    currIn.close();
+                                    resourceTransformed = true;
+                                    break;
+                                }
+                            }
+                        }
+                        //if not handled by transformer, add (once) to duplicates jar
+                        if ( !resourceTransformed )
+                        {
+                            if ( !duplicatesAdded.contains( lName ) )
+                            {
+                                duplicatesAdded.add( lName );
+                                ZipEntry entry = new ZipEntry( lName );
+                                duplicateZos.putNextEntry( entry );
+                                InputStream currIn = new FileInputStream( f );
+                                copyStreamWithoutClosing( currIn, duplicateZos );
+                                currIn.close();
+                                duplicateZos.closeEntry();
+                            }
+                        }
+                        f.delete();
+                    }
+                }
+            }
+        }
+        catch ( IOException e )
+        {
+            getLog().error( "Cannot removing duplicates : " + e.getMessage() );
+        }
+    }
+
     /**
      * Copies an input stream into an output stream but does not close the streams.
      *

src/test/java/com/jayway/maven/plugins/android/phase09package/ExtractDuplicatesIT.java → src/test/java/com/simpligility/maven/plugins/android/phase09package/ExtractDuplicatesIT.java

@@ -1,19 +1,4 @@
-/*
- * Copyright (C) 2014 simpligility technologies inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package com.jayway.maven.plugins.android.phase09package;
+package com.simpligility.maven.plugins.android.phase09package;
 
 import io.takari.maven.testing.TestResources;
 import io.takari.maven.testing.executor.MavenExecutionResult;
@@ -58,15 +43,17 @@ public void buildDeployAndRun() throws Exception {
         result.assertErrorFreeLog();
         result.assertLogText( "Duplicate file resourceA" );
         result.assertLogText( "Duplicate file resourceB" );
+        result.assertLogText( "Duplicate file resourceC" );
         File apk = new File(result.getBasedir().getAbsolutePath()+"/duplicates-app/target", "duplicates-app.apk");
         assertNotNull("APK Not Null", apk);
         ZipFile apkFile = new ZipFile(apk);
         assertNotNull(apkFile.getEntry("resourceA"));
         assertNotNull(apkFile.getEntry("resourceB"));
+        assertNotNull(apkFile.getEntry("resourceC"));
 
         //test services
         assertEntryContents(apkFile, "META-INF/services/com.jayway.maven.plugins.android.TestInterface",
-                "ImplementationA\nImplementationB\nImplementationC");
+                "ImplementationA\nImplementationB\nImplementationC\nImplementationApp");
 
         //test xpath xml
         assertEntryContents( apkFile, "META-INF/kmodule.xml", expectedKmodule );

src/test/projects/duplicates/duplicates-app/src/main/resources/META-INF/services/com.jayway.maven.plugins.android.TestInterface

@@ -0,0 +1 @@
+ImplementationApp

src/test/projects/duplicates/duplicates-app/src/main/resources/resourceC

@@ -0,0 +1 @@
+test content

src/test/projects/duplicates/duplicates-lib-b/src/main/resources/resourceC

@@ -0,0 +1 @@
+test content