diff --git a/composer/Plugin/Scaffold/Handler.php b/composer/Plugin/Scaffold/Handler.php
index e96b6f3820..ce4ca80820 100644
--- a/composer/Plugin/Scaffold/Handler.php
+++ b/composer/Plugin/Scaffold/Handler.php
@@ -161,6 +161,23 @@ public function scaffold() {
     // take priority and which are conjoined.
     $scaffold_files = new ScaffoldFileCollection($file_mappings, $location_replacements);
 
+    // Check to see if there are any scaffold files from a previous run that
+    // have been modified.
+    $hash_manager = HashManager::create($this->io, $this->composer->getConfig()->get('vendor-dir'), getcwd());
+
+    // Get the scaffold files that have been modified since they were written.
+    $modified = $hash_manager->getModified($scaffold_files);
+
+    // Ask the user what to do about the modified files (if any).
+    // Prompt the user and ask what to do about modified files.
+    $modified = $hash_manager->decideHowToHandleModified($modified);
+
+    // Remove the modified files if so instructed by the user. If nothing was
+    // modified, or the user did not want to keep any files, then this list
+    // will be empty.
+    $message = '  - Preserve <info>[dest-rel-path]</info>: modified by user.';
+    $scaffold_files->skipFiles($modified, $message);
+
     // Process the list of scaffolded files.
     $scaffold_results = ScaffoldFileCollection::process($scaffold_files, $this->io, $scaffold_options);
 
@@ -178,6 +195,9 @@ public function scaffold() {
 
     // Call post-scaffold scripts.
     $dispatcher->dispatch(self::POST_DRUPAL_SCAFFOLD_CMD);
+
+    // Save a hash for all of the scaffold result files.
+    $hash_manager->storeResultsHash($scaffold_results);
   }
 
   /**
diff --git a/composer/Plugin/Scaffold/HashManager.php b/composer/Plugin/Scaffold/HashManager.php
new file mode 100644
index 0000000000..b8e0e00338
--- /dev/null
+++ b/composer/Plugin/Scaffold/HashManager.php
@@ -0,0 +1,282 @@
+<?php
+
+namespace Drupal\Composer\Plugin\Scaffold;
+
+use Composer\IO\IOInterface;
+use Drupal\Composer\Plugin\Scaffold\Operations\ScaffoldFileCollection;
+use Composer\Json\JsonFile;
+
+/**
+ * Keeps a record of scaffold files and their hash values to detect changes.
+ */
+class HashManager {
+
+  /**
+   * Path to the vendor directory.
+   *
+   * @var string
+   */
+  protected $vendorDir;
+
+  /**
+   * Composer's I/O service.
+   *
+   * @var \Composer\IO\IOInterface
+   */
+  protected $io;
+
+  /**
+   * The directory where the project is located.
+   *
+   * @var string
+   */
+  protected $dir;
+
+  /**
+   * Cached list of hashes.
+   */
+  protected $hashCache = [];
+
+  /**
+   * Constructs a HashManager.
+   *
+   * Use HashManager::create instead.
+   *
+   * @param \Composer\IO\IOInterface $io
+   *   The input/output object.
+   * @param string $vendor_dir
+   *   The location of the vendor directory.
+   * @param string $dir
+   *   The directory where the project is located.
+   */
+  private function __construct(IOInterface $io, $vendor_dir, $dir) {
+    $this->io = $io;
+    $this->vendorDir = $vendor_dir;
+    $this->dir = $dir;
+  }
+
+  /**
+   * Creates a HashManager.
+   *
+   * @param \Composer\IO\IOInterface $io
+   *   The input/output object.
+   * @param string $vendor_dir
+   *   The location of the vendor directory.
+   * @param string $dir
+   *   The directory where the project is located.
+   *
+   * @return static
+   *   A loaded hash manager.
+   */
+  public static function create(IOInterface $io, $vendor_dir, $dir) {
+    $hash_manager = new static($io, $vendor_dir, $dir);
+    $hash_path = $hash_manager->pathToHashCache();
+    if (file_exists($hash_path)) {
+      $hash_manager->hashCache = json_decode(file_get_contents($hash_path), TRUE);
+    }
+    return $hash_manager;
+  }
+
+  /**
+   * Returns the list of scaffold files which have been modified.
+   *
+   * If a scaffold file exists on disk, and it also has an entry in the hash
+   * manager (because it was scaffolded on a previous run), then we will check
+   * to see if its hash value has changed. Any file with a modified hash value
+   * will be included in the result of this method.
+   *
+   * @param \Drupal\Composer\Plugin\Scaffold\Operations\ScaffoldFileCollection $scaffold_files
+   *   Collection of destination paths.
+   *
+   * @return string[]
+   *   List of modified files.
+   */
+  public function getModified(ScaffoldFileCollection $scaffold_files) {
+    // Iterate over our scaffold files and determine if any were modified.
+    $checked = [];
+    $modified = [];
+    foreach ($scaffold_files as $project_name => $project_files) {
+      foreach ($project_files as $destination_rel_path => $scaffold_file) {
+        if (!in_array($destination_rel_path, $checked)) {
+          $checked[] = $destination_rel_path;
+          if ($this->checkModified($scaffold_file->destination())) {
+            $modified[] = $destination_rel_path;
+          }
+        }
+      }
+    }
+
+    // Let the caller know what the user decided to keep.
+    return $modified;
+  }
+
+  /**
+   * Checks to see if a single scaffold file has been modified on disk.
+   *
+   * If the file existed on the last run and its hash has changed, then add it
+   * to the list of modified files.
+   *
+   * @param \Drupal\Composer\Plugin\Scaffold\ScaffoldFilePath $scaffold_file
+   *   One scaffold file that is about to be placed.
+   *
+   * @return bool
+   *   True if file has been modified since it was scaffolded.
+   */
+  protected function checkModified(ScaffoldFilePath $scaffold_file) {
+    $relative = $scaffold_file->relativePath();
+    if (!isset($this->hashCache[$relative])) {
+      return FALSE;
+    }
+    $hash = $this->hashFile($scaffold_file);
+    if (empty($hash)) {
+      return FALSE;
+    }
+    return $hash != $this->hashCache[$relative];
+  }
+
+  /**
+   * Asks the user how to handle modified files.
+   *
+   * As a side effect of this function, the root-level composer.json file will
+   * be modified if the user selects the "keep" option.
+   *
+   * @param string[] $modified
+   *   An array of destination paths that were modified.
+   *
+   * @return string[]
+   *   An array of modified that should not be preserved.
+   */
+  public function decideHowToHandleModified($modified) {
+    // Nothing modified? Nothing to do.
+    if (empty($modified)) {
+      return [];
+    }
+
+    // Show the user which files are in danger of being overwritten.
+    $show_modified = implode("\n", array_map(function ($item) {
+      return "  - <info>$item</info>";
+    }, $modified));
+    $this->io->writeError("The following managed scaffold files have been modified:\n$show_modified\n");
+
+    // Ask the user what they want to do
+    while (TRUE) {
+      $default = $this->defaultAnswerForModifiedPrompt();
+
+      // @todo: Composer also offers 'v' (view) and 'd' (diff); we could add
+      // 'view' as a follow-on task, but 'diff' would be difficult here.
+      switch ($this->io->ask('    <info>Discard changes [y,n,k,a,?]?</info> ', $default)) {
+        case 'y':
+          return [];
+
+        case 'n':
+          return $modified;
+
+        case 'k':
+          $this->overrideModifiedInComposerJson($modified);
+          return $modified;
+
+        case 'a':
+          throw new \RuntimeException('Scaffold aborted');
+
+        case '?':
+        default:
+          $this->io->writeError([
+              '    y - discard changes and rewrite scaffold files',
+              '    n - keep modified files in their current state; ask again the next time Composer runs',
+              '    k - keep modified files and modify composer.json to avoid being asked again',
+              '    a - abort scaffold operation',
+              '    For information on how to manage scaffold modifications, see:',
+              '    https://www.drupal.org/docs/develop/using-composer/using-drupals-composer-scaffold',
+          ]);
+      }
+    }
+  }
+
+  /**
+   * Determines what our default action should be for prompt.
+   *
+   * The default value is returned automatically in non-interactive mode, or
+   * if the user hits [RETURN] without making a selection.
+   *
+   * @return string
+   *   Default value to return from 'modified' prompt.
+   */
+  protected function defaultAnswerForModifiedPrompt() {
+    // Interactive? Ignore environment variables and always default to '?'.
+    if ($this->io->isInteractive()) {
+      return '?';
+    }
+    // Keep modified files and don't ask again.
+    if (getenv('DRUPAL_SCAFFOLD_KEEP_MODIFIED')) {
+      return 'k';
+    }
+    // Discard modified if instructed.
+    if (getenv('DRUPAL_SCAFFOLD_DISCARD_MODIFIED')) {
+      return 'y';
+    }
+    // Default is preserve modified files and ask again next time.
+    return 'n';
+  }
+
+  /**
+   * Modifies composer.json to preserve modified files on subsequent runs.
+   *
+   * @param array $modified
+   *   List of modified packages to disable in the composer.json file mappings.
+   */
+  protected function overrideModifiedInComposerJson(array $modified) {
+    $composer_json_file = new JsonFile($this->dir . '/composer.json');
+
+    $composer_json_data = $composer_json_file->read();
+    foreach ($modified as $keepPackage) {
+      $composer_json_data['extra']['drupal-scaffold']['file-mapping'][$keepPackage] = FALSE;
+    }
+    $composer_json_file->write($composer_json_data);
+  }
+
+  /**
+   * Stores the provided list of file paths to the hash cache file.
+   *
+   * @param \Drupal\Composer\Plugin\Scaffold\Operations\ScaffoldResult[] $files
+   *   A list of scaffold results, each of which holds a path.
+   */
+  public function storeResultsHash(array $files) {
+    foreach ($files as $scaffold_result) {
+      if ($scaffold_result->isManaged()) {
+        $hash = $this->hashFile($scaffold_result->destination());
+        $relative = $scaffold_result->destination()->relativePath();
+        $this->hashCache[$relative] = $hash;
+      }
+    }
+    $hash_path = $this->pathToHashCache();
+    file_put_contents($hash_path, json_encode($this->hashCache));
+  }
+
+  /**
+   * Gets the path to the file where the list of hashes is stored.
+   *
+   * @return string
+   *   Path where the list of scaffolded files and their hashes are stored.
+   */
+  protected function pathToHashCache() {
+    return "{$this->vendorDir}/drupal/scaffolded.json";
+  }
+
+  /**
+   * Calculates the on-disk hash value of a scaffold file.
+   *
+   * @param \Drupal\Composer\Plugin\Scaffold\ScaffoldFilePath $scaffold_file
+   *   Path to the scaffold file, at its destination path.
+   *
+   * @return string
+   *   Hash value.
+   */
+  protected function hashFile(ScaffoldFilePath $scaffold_file) {
+    $path = $scaffold_file->fullPath();
+    if (!file_exists($path)) {
+      return '';
+    }
+    return sha1_file($path);
+  }
+
+}
diff --git a/composer/Plugin/Scaffold/Operations/ScaffoldFileCollection.php b/composer/Plugin/Scaffold/Operations/ScaffoldFileCollection.php
index c000e64a47..bff67dd32c 100644
--- a/composer/Plugin/Scaffold/Operations/ScaffoldFileCollection.php
+++ b/composer/Plugin/Scaffold/Operations/ScaffoldFileCollection.php
@@ -72,11 +72,33 @@ public function __construct(array $file_mappings, Interpolator $location_replace
     }
   }
 
+  /**
+   * Filter out any item in the list whose destination path has been modified.
+   *
+   * @param array $files_to_skip
+   *   List of destination paths
+   * @param string $message
+   *   Explanation of why files were skipped
+   */
+  public function skipFiles($files_to_skip, $message) {
+    $op = new SkipOp($message);
+
+    // If we were instructed to keep modified files, then filter them out of our
+    // list of scaffold files to process.
+    foreach ($this->scaffoldFilesByProject as $project_name => $scaffold_files) {
+      foreach ($scaffold_files as $destination_rel_path => $scaffold_file) {
+        if (in_array($destination_rel_path, $files_to_skip)) {
+          $this->scaffoldFilesByProject[$project_name][$destination_rel_path] = new ScaffoldFileInfo($scaffold_file->destination(), $op);
+        }
+      }
+    }
+  }
+
   /**
    * {@inheritdoc}
    */
   public function getIterator() {
-    return new \RecursiveArrayIterator($this->scaffoldFilesByProject, \RecursiveArrayIterator::CHILD_ARRAYS_ONLY);
+    return new \ArrayIterator($this->scaffoldFilesByProject);
   }
 
   /**
diff --git a/core/tests/Drupal/Tests/Composer/Plugin/Scaffold/Functional/ComposerHookTest.php b/core/tests/Drupal/Tests/Composer/Plugin/Scaffold/Functional/ComposerHookTest.php
index c8e18e1b03..870f5703c7 100644
--- a/core/tests/Drupal/Tests/Composer/Plugin/Scaffold/Functional/ComposerHookTest.php
+++ b/core/tests/Drupal/Tests/Composer/Plugin/Scaffold/Functional/ComposerHookTest.php
@@ -26,16 +26,6 @@ class ComposerHookTest extends TestCase {
   use ExecTrait;
   use AssertUtilsTrait;
 
-  /**
-   * The root of this project.
-   *
-   * Used to substitute this project's base directory into composer.json files
-   * so Composer can find it.
-   *
-   * @var string
-   */
-  protected $projectRoot;
-
   /**
    * Directory to perform the tests in.
    *
@@ -64,7 +54,9 @@ protected function setUp() {
     $this->fileSystem = new Filesystem();
     $this->fixtures = new Fixtures();
     $this->fixtures->createIsolatedComposerCacheDir();
-    $this->projectRoot = $this->fixtures->projectRoot();
+    $this->fixturesDir = $this->fixtures->tmpDir($this->getName());
+    $replacements = ['SYMLINK' => 'false', 'PROJECT_ROOT' => $this->fixtures->projectRoot()];
+    $this->fixtures->cloneFixtureProjects($this->fixturesDir, $replacements);
   }
 
   /**
@@ -76,46 +68,173 @@ protected function tearDown() {
   }
 
   /**
-   * Test to see if scaffold operation runs at the correct times.
+   * Test to see if scaffold operation runs after 'composer require'.
    */
-  public function testComposerHooks() {
-    $this->fixturesDir = $this->fixtures->tmpDir($this->getName());
-    $replacements = ['SYMLINK' => 'false', 'PROJECT_ROOT' => $this->projectRoot];
-    $this->fixtures->cloneFixtureProjects($this->fixturesDir, $replacements);
+  public function testRequireHooks() {
     $topLevelProjectDir = 'composer-hooks-fixture';
     $sut = $this->fixturesDir . '/' . $topLevelProjectDir;
+
     // First test: run composer install. This is the same as composer update
     // since there is no lock file. Ensure that scaffold operation ran.
     $this->mustExec("composer install --no-ansi", $sut);
     $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+
     // Run composer required to add in the scaffold-override-fixture. This
     // project is "allowed" in our main fixture project, but not required.
     // We expect that requiring this library should re-scaffold, resulting
     // in a changed default.settings.php file.
     $stdout = $this->mustExec("composer require --no-ansi --no-interaction fixtures/scaffold-override-fixture:dev-master", $sut);
     $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'scaffolded from the scaffold-override-fixture');
+
     // Make sure that the appropriate notice informing us that scaffolding
     // is allowed was printed.
     $this->assertContains('Package fixtures/scaffold-override-fixture has scaffold operations, and is already allowed in the root-level composer.json file.', $stdout);
+  }
+
+  /**
+   * Tests to see if deleted / modified files are handled correctly.
+   */
+  public function testDeletedAndModifiedScaffoldFiles() {
+    $topLevelProjectDir = 'composer-hooks-fixture';
+    $sut = $this->fixturesDir . '/' . $topLevelProjectDir;
+
+    // Run 'composer install' again to set up for our next set of tests.
+    $this->mustExec("composer install --no-ansi", $sut);
+
     // Delete one scaffold file, just for test purposes, then run
     // 'composer update' and see if the scaffold file is replaced.
     @unlink($sut . '/sites/default/default.settings.php');
     $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
     $this->mustExec("composer update --no-ansi", $sut);
-    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'scaffolded from the scaffold-override-fixture');
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+
     // Delete the same test scaffold file again, then run
     // 'composer drupal:scaffold' and see if the scaffold file is
     // re-scaffolded.
     @unlink($sut . '/sites/default/default.settings.php');
     $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
     $this->mustExec("composer install --no-ansi", $sut);
-    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'scaffolded from the scaffold-override-fixture');
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+
     // Delete the same test scaffold file yet again, then run
     // 'composer install' and see if the scaffold file is re-scaffolded.
     @unlink($sut . '/sites/default/default.settings.php');
     $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
     $this->mustExec("composer drupal:scaffold --no-ansi", $sut);
-    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'scaffolded from the scaffold-override-fixture');
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+
+    // Modify the same test scaffold file, then run 'composer drupal:scaffold'
+    // and confirm the modification is not overwritten.
+    $contents = file_get_contents($sut . '/sites/default/default.settings.php');
+    file_put_contents($sut . '/sites/default/default.settings.php', $contents . "\n// Simulated user modification\n");
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut);
+    $this->assertContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+    $post_scaffold_contents = file_get_contents($sut . '/sites/default/default.settings.php');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents);
+
+    // Run 'composer drupal:scaffold' twice in a row to make sure that the
+    // hash file of the modified file is retained, such that drupal:scaffold
+    // still recognizes that the modified file is modified.
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut);
+    $this->assertContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+    $post_scaffold_contents_two = file_get_contents($sut . '/sites/default/default.settings.php');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents_two);
+
+    // Finally, run 'composer drupal:scaffold' yet a third time in a row, this
+    // time with an environment variable set that tells drupal:scaffold to act
+    // as if the user had requested that modified files be overwritten.
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut, ['DRUPAL_SCAFFOLD_DISCARD_MODIFIED' => 1]);
+    $this->assertContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+    $post_scaffold_contents_three = file_get_contents($sut . '/sites/default/default.settings.php');
+    $this->assertNotContains('Simulated user modification', $post_scaffold_contents_three);
+
+    // And if we run it yet again, then the file should not be modified.
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut);
+    $this->assertNotContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+    $post_scaffold_contents_three = file_get_contents($sut . '/sites/default/default.settings.php');
+    $this->assertNotContains('Simulated user modification', $post_scaffold_contents_three);
+
+    // Modify the test scaffold file even again, then run
+    // 'composer drupal:scaffold' with DRUPAL_SCAFFOLD_KEEP_MODIFIED. Confirm
+    // that the file is now excluded in the composer.json file's file-mapping.
+    $contents = file_get_contents($sut . '/sites/default/default.settings.php');
+    file_put_contents($sut . '/sites/default/default.settings.php', $contents . "\n// Simulated user modification\n");
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut, ['DRUPAL_SCAFFOLD_KEEP_MODIFIED' => 1]);
+    $this->assertContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+    $post_scaffold_contents = file_get_contents($sut . '/sites/default/default.settings.php');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents);
+    $post_scaffold_composer_json = file_get_contents($sut . '/composer.json');
+    $this->assertContains('"[web-root]/sites/default/default.settings.php": false', $post_scaffold_composer_json);
+
+    // Scaffold again. We should not modify the files we kept
+    // (default.settings.php) above.
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut, ['DRUPAL_SCAFFOLD_DISCARD_MODIFIED' => 1]);
+    $this->assertNotContains("The following managed scaffold files have been modified:\n  - [web-root]/sites/default/default.settings.php", $stdout);
+  }
+
+  /**
+   * Tests deleting and modifying two different scaffold files at the same time.
+   */
+  public function testDeletingAndModifyingAtSameTime() {
+    $topLevelProjectDir = 'composer-hooks-fixture';
+    $sut = $this->fixturesDir . '/' . $topLevelProjectDir;
+
+    // Run 'composer install' again to set up for our next set of tests.
+    $this->mustExec("composer install --no-ansi", $sut);
+
+    // Delete 'default.settings.php' and modify 'robots.txt', then run
+    // the scaffold operation and see if the default settings file comes back,
+    // and the robots.txt file modification is preserved.
+    @unlink($sut . '/sites/default/default.settings.php');
+    $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
+    $contents = file_get_contents($sut . '/robots.txt');
+    file_put_contents($sut . '/robots.txt', $contents . "\n# Simulated user modification\n");
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut);
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+    $post_scaffold_contents = file_get_contents($sut . '/robots.txt');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents);
+
+    // Run the same test again to ensure that the scaffold tool still
+    // understands that the deleted file is managed.
+    @unlink($sut . '/sites/default/default.settings.php');
+    $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut);
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+    $post_scaffold_contents = file_get_contents($sut . '/robots.txt');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents);
+
+    // Make the same modifications again, but this time we will run the scaffold
+    // command with 'DRUPAL_SCAFFOLD_DISCARD_MODIFIED' environment variable,
+    // simulating the user selecting 'y' from the "discard modified" prompt.
+    // Make sure that both files go back the way they were.
+    @unlink($sut . '/sites/default/default.settings.php');
+    $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
+    $contents = file_get_contents($sut . '/robots.txt');
+    file_put_contents($sut . '/robots.txt', $contents . "\n# Simulated user modification\n");
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut, ['DRUPAL_SCAFFOLD_DISCARD_MODIFIED' => 1]);
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+    $post_scaffold_contents = file_get_contents($sut . '/robots.txt');
+    $this->assertNotContains('Simulated user modification', $post_scaffold_contents);
+
+    // Now we'll do it again with 'DRUPAL_SCAFFOLD_KEEP_MODIFIED', to simulate
+    // answering 'keep' to the "discard modified" prompt. Confirm that the
+    // composer.json file is modified.
+    @unlink($sut . '/sites/default/default.settings.php');
+    $this->assertFileNotExists($sut . '/sites/default/default.settings.php');
+    $contents = file_get_contents($sut . '/robots.txt');
+    file_put_contents($sut . '/robots.txt', $contents . "\n# Simulated user modification\n");
+    $stdout = $this->mustExec("composer drupal:scaffold --no-ansi --no-interaction 2>&1", $sut, ['DRUPAL_SCAFFOLD_KEEP_MODIFIED' => 1]);
+    $this->assertScaffoldedFile($sut . '/sites/default/default.settings.php', FALSE, 'Test version of default.settings.php from drupal/core');
+    $post_scaffold_contents = file_get_contents($sut . '/robots.txt');
+    $this->assertContains('Simulated user modification', $post_scaffold_contents);
+    $post_scaffold_composer_json = file_get_contents($sut . '/composer.json');
+    $this->assertContains('"[web-root]/robots.txt": false', $post_scaffold_composer_json);
+  }
+
+  /**
+   * Tests to see if create-project scaffolds correctly.
+   */
+  public function testCreateProject() {
     // Run 'composer create-project' to create a new test project called
     // 'create-project-test', which is a copy of 'fixtures/drupal-drupal'.
     $sut = $this->fixturesDir . '/create-project-test';
@@ -127,8 +246,10 @@ public function testComposerHooks() {
     $this->assertScaffoldedFile($sut . '/index.php', FALSE, 'Test version of index.php from drupal/core');
     $topLevelProjectDir = 'composer-hooks-nothing-allowed-fixture';
     $sut = $this->fixturesDir . '/' . $topLevelProjectDir;
+
     // Run composer install on an empty project.
     $this->mustExec("composer install --no-ansi", $sut);
+
     // Require a project that is not allowed to scaffold and confirm that we
     // get a warning, and it does not scaffold.
     $stdout = $this->mustExec("composer require --no-ansi --no-interaction fixtures/scaffold-override-fixture:dev-master", $sut);