diff --git a/src/Composer/Autoload/AutoloadGenerator.php b/src/Composer/Autoload/AutoloadGenerator.php
index 4a55a53c0..7227166a8 100644
--- a/src/Composer/Autoload/AutoloadGenerator.php
+++ b/src/Composer/Autoload/AutoloadGenerator.php
@@ -252,14 +252,20 @@ EOF;
         file_put_contents($targetDir.'/autoload_namespaces.php', $namespacesFile);
         file_put_contents($targetDir.'/autoload_psr4.php', $psr4File);
         file_put_contents($targetDir.'/autoload_classmap.php', $classmapFile);
-        if ($includePathFile = $this->getIncludePathsFile($packageMap, $filesystem, $basePath, $vendorPath, $vendorPathCode52, $appBaseDirCode)) {
-            file_put_contents($targetDir.'/include_paths.php', $includePathFile);
+        $includePathFilePath = $targetDir.'/include_paths.php';
+        if ($includePathFileContents = $this->getIncludePathsFile($packageMap, $filesystem, $basePath, $vendorPath, $vendorPathCode52, $appBaseDirCode)) {
+            file_put_contents($includePathFilePath, $includePathFileContents);
+        } else if (file_exists($includePathFilePath)){
+            unlink($includePathFilePath);
         }
-        if ($includeFilesFile = $this->getIncludeFilesFile($autoloads['files'], $filesystem, $basePath, $vendorPath, $vendorPathCode52, $appBaseDirCode)) {
-            file_put_contents($targetDir.'/autoload_files.php', $includeFilesFile);
+        $includeFilesFilePath = $targetDir.'/autoload_files.php';
+        if ($includeFilesFileContents = $this->getIncludeFilesFile($autoloads['files'], $filesystem, $basePath, $vendorPath, $vendorPathCode52, $appBaseDirCode)) {
+            file_put_contents($includeFilesFilePath, $includeFilesFileContents);
+        } else if (file_exists($includeFilesFilePath)) {
+            unlink($includeFilesFilePath);
         }
         file_put_contents($vendorPath.'/autoload.php', $this->getAutoloadFile($vendorPathToTargetDirCode, $suffix));
-        file_put_contents($targetDir.'/autoload_real.php', $this->getAutoloadRealFile(true, (bool) $includePathFile, $targetDirLoader, (bool) $includeFilesFile, $vendorPathCode, $appBaseDirCode, $suffix, $useGlobalIncludePath, $prependAutoloader, $classMapAuthoritative));
+        file_put_contents($targetDir.'/autoload_real.php', $this->getAutoloadRealFile(true, (bool) $includePathFileContents, $targetDirLoader, (bool) $includeFilesFileContents, $vendorPathCode, $appBaseDirCode, $suffix, $useGlobalIncludePath, $prependAutoloader, $classMapAuthoritative));
 
         $this->safeCopy(__DIR__.'/ClassLoader.php', $targetDir.'/ClassLoader.php');
         $this->safeCopy(__DIR__.'/../../../LICENSE', $targetDir.'/LICENSE');
diff --git a/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php b/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
index dbb7d2fad..007f16363 100644
--- a/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
+++ b/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
@@ -585,6 +585,71 @@ class AutoloadGeneratorTest extends TestCase
         $this->assertTrue(function_exists('testFilesAutoloadGenerationRoot'));
     }
 
+    public function testFilesAutoloadGenerationRemoveExtraEntitiesFromAutoloadFiles()
+    {
+        $autoloadPackage = new Package('a', '1.0', '1.0');
+        $autoloadPackage->setAutoload(array('files' => array('root.php')));
+        $autoloadPackage->setIncludePaths(array('/lib', '/src'));
+
+        $notAutoloadPackage = new Package('a', '1.0', '1.0');
+
+        $autoloadPackages = array();
+        $autoloadPackages[] = $a = new Package('a/a', '1.0', '1.0');
+        $autoloadPackages[] = $b = new Package('b/b', '1.0', '1.0');
+        $autoloadPackages[] = $c = new Package('c/c', '1.0', '1.0');
+        $a->setAutoload(array('files' => array('test.php')));
+        $a->setIncludePaths(array('lib1', 'src1'));
+        $b->setAutoload(array('files' => array('test2.php')));
+        $b->setIncludePaths(array('lib2'));
+        $c->setAutoload(array('files' => array('test3.php', 'foo/bar/test4.php')));
+        $c->setIncludePaths(array('lib3'));
+        $c->setTargetDir('foo/bar');
+
+        $notAutoloadPackages = array();
+        $notAutoloadPackages[] = $a = new Package('a/a', '1.0', '1.0');
+        $notAutoloadPackages[] = $b = new Package('b/b', '1.0', '1.0');
+        $notAutoloadPackages[] = $c = new Package('c/c', '1.0', '1.0');
+
+        $this->repository->expects($this->at(0))
+            ->method('getCanonicalPackages')
+            ->will($this->returnValue($autoloadPackages));
+
+        $this->repository->expects($this->at(1))
+            ->method('getCanonicalPackages')
+            ->will($this->returnValue($notAutoloadPackages));
+
+        $this->repository->expects($this->at(2))
+            ->method('getCanonicalPackages')
+            ->will($this->returnValue($notAutoloadPackages));
+
+        $this->fs->ensureDirectoryExists($this->vendorDir.'/a/a');
+        $this->fs->ensureDirectoryExists($this->vendorDir.'/b/b');
+        $this->fs->ensureDirectoryExists($this->vendorDir.'/c/c/foo/bar');
+        file_put_contents($this->vendorDir.'/a/a/test.php', '<?php function testFilesAutoloadGeneration1() {}');
+        file_put_contents($this->vendorDir.'/b/b/test2.php', '<?php function testFilesAutoloadGeneration2() {}');
+        file_put_contents($this->vendorDir.'/c/c/foo/bar/test3.php', '<?php function testFilesAutoloadGeneration3() {}');
+        file_put_contents($this->vendorDir.'/c/c/foo/bar/test4.php', '<?php function testFilesAutoloadGeneration4() {}');
+        file_put_contents($this->workingDir.'/root.php', '<?php function testFilesAutoloadGenerationRoot() {}');
+
+        $this->generator->dump($this->config, $this->repository, $autoloadPackage, $this->im, 'composer', false, 'FilesAutoload');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_functions.php', $this->vendorDir.'/autoload.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_real_functions_with_include_paths.php', $this->vendorDir.'/composer/autoload_real.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_files_functions.php', $this->vendorDir.'/composer/autoload_files.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/include_paths_functions.php', $this->vendorDir.'/composer/include_paths.php');
+
+        $this->generator->dump($this->config, $this->repository, $autoloadPackage, $this->im, 'composer', false, 'FilesAutoload');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_functions.php', $this->vendorDir.'/autoload.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_real_functions_with_include_paths.php', $this->vendorDir.'/composer/autoload_real.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_files_functions_with_removed_extra.php', $this->vendorDir.'/composer/autoload_files.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/include_paths_functions_with_removed_extra.php', $this->vendorDir.'/composer/include_paths.php');
+
+        $this->generator->dump($this->config, $this->repository, $notAutoloadPackage, $this->im, 'composer', false, 'FilesAutoload');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_functions.php', $this->vendorDir.'/autoload.php');
+        $this->assertFileEquals(__DIR__.'/Fixtures/autoload_real_functions_with_removed_include_paths_and_autolad_files.php', $this->vendorDir.'/composer/autoload_real.php');
+        $this->assertFileNotExists($this->vendorDir.'/composer/autoload_files.php');
+        $this->assertFileNotExists($this->vendorDir.'/composer/include_paths.php');
+    }
+
     public function testFilesAutoloadOrderByDependencies()
     {
         $package = new Package('a', '1.0', '1.0');
diff --git a/tests/Composer/Test/Autoload/Fixtures/autoload_files_functions_with_removed_extra.php b/tests/Composer/Test/Autoload/Fixtures/autoload_files_functions_with_removed_extra.php
new file mode 100644
index 000000000..8d124df37
--- /dev/null
+++ b/tests/Composer/Test/Autoload/Fixtures/autoload_files_functions_with_removed_extra.php
@@ -0,0 +1,10 @@
+<?php
+
+// autoload_files.php @generated by Composer
+
+$vendorDir = dirname(dirname(__FILE__));
+$baseDir = dirname($vendorDir);
+
+return array(
+    $baseDir . '/root.php',
+);
diff --git a/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_include_paths.php b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_include_paths.php
new file mode 100644
index 000000000..68fb6ecbf
--- /dev/null
+++ b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_include_paths.php
@@ -0,0 +1,59 @@
+<?php
+
+// autoload_real.php @generated by Composer
+
+class ComposerAutoloaderInitFilesAutoload
+{
+    private static $loader;
+
+    public static function loadClassLoader($class)
+    {
+        if ('Composer\Autoload\ClassLoader' === $class) {
+            require __DIR__ . '/ClassLoader.php';
+        }
+    }
+
+    public static function getLoader()
+    {
+        if (null !== self::$loader) {
+            return self::$loader;
+        }
+
+        spl_autoload_register(array('ComposerAutoloaderInitFilesAutoload', 'loadClassLoader'), true, true);
+        self::$loader = $loader = new \Composer\Autoload\ClassLoader();
+        spl_autoload_unregister(array('ComposerAutoloaderInitFilesAutoload', 'loadClassLoader'));
+
+        $includePaths = require __DIR__ . '/include_paths.php';
+        array_push($includePaths, get_include_path());
+        set_include_path(join(PATH_SEPARATOR, $includePaths));
+
+        $map = require __DIR__ . '/autoload_namespaces.php';
+        foreach ($map as $namespace => $path) {
+            $loader->set($namespace, $path);
+        }
+
+        $map = require __DIR__ . '/autoload_psr4.php';
+        foreach ($map as $namespace => $path) {
+            $loader->setPsr4($namespace, $path);
+        }
+
+        $classMap = require __DIR__ . '/autoload_classmap.php';
+        if ($classMap) {
+            $loader->addClassMap($classMap);
+        }
+
+        $loader->register(true);
+
+        $includeFiles = require __DIR__ . '/autoload_files.php';
+        foreach ($includeFiles as $file) {
+            composerRequireFilesAutoload($file);
+        }
+
+        return $loader;
+    }
+}
+
+function composerRequireFilesAutoload($file)
+{
+    require $file;
+}
diff --git a/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_removed_include_paths_and_autolad_files.php b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_removed_include_paths_and_autolad_files.php
new file mode 100644
index 000000000..205cd7158
--- /dev/null
+++ b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions_with_removed_include_paths_and_autolad_files.php
@@ -0,0 +1,50 @@
+<?php
+
+// autoload_real.php @generated by Composer
+
+class ComposerAutoloaderInitFilesAutoload
+{
+    private static $loader;
+
+    public static function loadClassLoader($class)
+    {
+        if ('Composer\Autoload\ClassLoader' === $class) {
+            require __DIR__ . '/ClassLoader.php';
+        }
+    }
+
+    public static function getLoader()
+    {
+        if (null !== self::$loader) {
+            return self::$loader;
+        }
+
+        spl_autoload_register(array('ComposerAutoloaderInitFilesAutoload', 'loadClassLoader'), true, true);
+        self::$loader = $loader = new \Composer\Autoload\ClassLoader();
+        spl_autoload_unregister(array('ComposerAutoloaderInitFilesAutoload', 'loadClassLoader'));
+
+        $map = require __DIR__ . '/autoload_namespaces.php';
+        foreach ($map as $namespace => $path) {
+            $loader->set($namespace, $path);
+        }
+
+        $map = require __DIR__ . '/autoload_psr4.php';
+        foreach ($map as $namespace => $path) {
+            $loader->setPsr4($namespace, $path);
+        }
+
+        $classMap = require __DIR__ . '/autoload_classmap.php';
+        if ($classMap) {
+            $loader->addClassMap($classMap);
+        }
+
+        $loader->register(true);
+
+        return $loader;
+    }
+}
+
+function composerRequireFilesAutoload($file)
+{
+    require $file;
+}
diff --git a/tests/Composer/Test/Autoload/Fixtures/include_paths_functions.php b/tests/Composer/Test/Autoload/Fixtures/include_paths_functions.php
new file mode 100644
index 000000000..f1095cf67
--- /dev/null
+++ b/tests/Composer/Test/Autoload/Fixtures/include_paths_functions.php
@@ -0,0 +1,15 @@
+<?php
+
+// include_paths.php @generated by Composer
+
+$vendorDir = dirname(dirname(__FILE__));
+$baseDir = dirname($vendorDir);
+
+return array(
+    $baseDir . '/lib',
+    $baseDir . '/src',
+    $vendorDir . '/a/a/lib1',
+    $vendorDir . '/a/a/src1',
+    $vendorDir . '/b/b/lib2',
+    $vendorDir . '/c/c/lib3',
+);
diff --git a/tests/Composer/Test/Autoload/Fixtures/include_paths_functions_with_removed_extra.php b/tests/Composer/Test/Autoload/Fixtures/include_paths_functions_with_removed_extra.php
new file mode 100644
index 000000000..4403b11ec
--- /dev/null
+++ b/tests/Composer/Test/Autoload/Fixtures/include_paths_functions_with_removed_extra.php
@@ -0,0 +1,11 @@
+<?php
+
+// include_paths.php @generated by Composer
+
+$vendorDir = dirname(dirname(__FILE__));
+$baseDir = dirname($vendorDir);
+
+return array(
+    $baseDir . '/lib',
+    $baseDir . '/src',
+);