diff --git a/phpunit.xml.dist b/phpunit.xml.dist
index 41cc73f..801d284 100644
--- a/phpunit.xml.dist
+++ b/phpunit.xml.dist
@@ -3,6 +3,7 @@
          xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/10.0/phpunit.xsd"
          bootstrap="vendor/autoload.php"
          colors="true"
+         displayDetailsOnTestsThatTriggerWarnings="true"
          displayDetailsOnPhpunitDeprecations="true">
   <testsuites>
     <testsuite name="Tests">
diff --git a/src/Composer/PatchAddCommand.php b/src/Composer/PatchAddCommand.php
index 53d1dee..fc08434 100644
--- a/src/Composer/PatchAddCommand.php
+++ b/src/Composer/PatchAddCommand.php
@@ -146,32 +146,15 @@ protected function execute(InputInterface $input, OutputInterface $output): int
     $output->writeln('The patch was successfully added.');
 
     if (!$input->getOption('no-update')) {
-      $application = $this->getApplication();
-      $application->setAutoExit(FALSE);
-
       if ($this->isComposerPatches1()) {
         // Trigger install command after adding a patch.
-        $install = Installer::create($this->getIO(), $this->requireComposer());
-        $install->setUpdate(TRUE)
-          // Forward the option
-          ->setVerbose($input->getOption('verbose'))
-          // Only update the current package
-          ->setUpdateAllowList([$package])
-          // Don't update the dependencies of the patched package.
-          ->setUpdateAllowTransitiveDependencies(Request::UPDATE_ONLY_LISTED)
-          // Patches are always considered to be applied in "dev mode".
-          // This is also required to prevent composer from removing all installed
-          // dev dependencies.
-          ->setDevMode($updateDevMode)
-          ->run();
+        $this->runReinstall($package, $updateDevMode);
       }
       else {
         $output->writeln('<info>Relocking patches...</info>');
-        $application->run(new ArrayInput(['command' => 'patches-relock']), $output);
+        $this->runPatchesRelock();
         $output->writeln('<info>Repatching dependencies...</info>');
-        $application->run(new ArrayInput(['command' => 'patches-repatch']), $output);
-        $output->writeln('<info>Reinstalling package...</info>');
-        $application->run(new ArrayInput(['command' => 'reinstall', 'packages' => [$package]]), $output);
+        $this->runRepatch();
       }
     }
 
diff --git a/src/Composer/PatchBaseCommand.php b/src/Composer/PatchBaseCommand.php
index 1e89caf..02c97d4 100644
--- a/src/Composer/PatchBaseCommand.php
+++ b/src/Composer/PatchBaseCommand.php
@@ -2,9 +2,14 @@
 
 namespace szeidler\ComposerPatchesCLI\Composer;
 
+use Composer\DependencyResolver\Operation\UninstallOperation;
 use Composer\Factory;
 use Composer\Command\BaseCommand;
+use Composer\Json\JsonFile;
 use Composer\Semver\Comparator;
+use Composer\Installer;
+use Composer\DependencyResolver\Request;
+use cweagans\Composer\Plugin\Patches;
 
 class PatchBaseCommand extends BaseCommand {
 
@@ -87,6 +92,93 @@ protected function isComposerPatches1() {
     return $version && version_compare($version, '2.0.0', '<');
   }
 
+  /**
+   * Get the Patches plugin instance.
+   */
+  protected function getPatchesPluginInstance() {
+    foreach ($this->requireComposer()->getPluginManager()->getPlugins() as $plugin) {
+      $className = get_class($plugin);
+      if (str_starts_with($className, 'cweagans\Composer\Plugin\Patches')) {
+        return $plugin;
+      }
+    }
+    return NULL;
+  }
+
+  /**
+   * Run the patches-relock command.
+   */
+  protected function runPatchesRelock(): void {
+    $plugin = $this->getPatchesPluginInstance();
+    if ($plugin) {
+      if (file_exists($plugin->getLockFile()->getPath())) {
+        unlink($plugin->getLockFile()->getPath());
+      }
+      $plugin->createNewPatchesLock();
+    }
+  }
+
+  /**
+   * Run the patches-repatch command.
+   */
+  protected function runRepatch(): void {
+    $plugin = $this->getPatchesPluginInstance();
+    if ($plugin) {
+      $plugin->loadLockedPatches();
+      $patchCollection = $plugin->getPatchCollection();
+      if ($patchCollection) {
+        $localRepository = $this->requireComposer()
+          ->getRepositoryManager()
+          ->getLocalRepository();
+
+        $patched_packages = $patchCollection->getPatchedPackages();
+        $packages = array_filter($localRepository->getPackages(), function ($val) use ($patched_packages) {
+          return in_array($val->getName(), $patched_packages);
+        });
+
+        $promises = [];
+        foreach ($packages as $package) {
+          $uninstallOperation = new UninstallOperation($package);
+          $promises[] = $this->requireComposer()
+            ->getInstallationManager()
+            ->uninstall($localRepository, $uninstallOperation);
+        }
+
+        $promises = array_filter($promises);
+        if (!empty($promises)) {
+          $this->requireComposer()->getLoop()->wait($promises);
+        }
+
+        $install = Installer::create($this->getIO(), $this->requireComposer());
+        $install->run();
+      }
+    }
+  }
+
+  /**
+   * Run the reinstall command for a package.
+   *
+   * @param string $package
+   * @param bool $devMode
+   */
+  protected function runReinstall(string $package, bool $devMode = TRUE): void {
+    $install = Installer::create($this->getIO(), $this->requireComposer());
+    $install->setUpdate(TRUE)
+      ->setUpdateAllowList([$package])
+      ->setUpdateAllowTransitiveDependencies(Request::UPDATE_ONLY_LISTED)
+      ->setDevMode($devMode)
+      ->run();
+  }
+
+  /**
+   * Updates the lock file hash.
+   */
+  protected function updateLockFile(): void {
+    $composerJsonPath = Factory::getComposerFile();
+    $composerJson = new JsonFile($composerJsonPath);
+    $this->requireComposer()->getLocker()->updateHash($composerJson);
+  }
+
   /**
    * Get the patches from root composer or external file
    *
diff --git a/src/Composer/PatchEnableCommand.php b/src/Composer/PatchEnableCommand.php
index 3c0d124..f7012f2 100644
--- a/src/Composer/PatchEnableCommand.php
+++ b/src/Composer/PatchEnableCommand.php
@@ -43,6 +43,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
       $patches_file = new JsonFile($patches_filename);
       if (!$patches_file->exists()) {
         if (copy(dirname(__FILE__) . '/../Fixtures/composer.patches.json', $patches_filename)) {
+          print_r(dirname(__FILE__));
           $output->writeln('The composer patches file was created.');
         }
         else {
diff --git a/src/Composer/PatchMigrateCommand.php b/src/Composer/PatchMigrateCommand.php
index c067614..5d6b62e 100644
--- a/src/Composer/PatchMigrateCommand.php
+++ b/src/Composer/PatchMigrateCommand.php
@@ -39,57 +39,10 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 
     if ($patchType === self::PATCHTYPE_ROOT_CP1) {
       $output->writeln('<info>Migrating patches from root composer.json...</info>');
-      
+
       // Move patches to the new location.
       $composer_manipulator->removeSubNode('extra', 'patches');
       $composer_manipulator->addSubNode('extra', 'composer-patches.patches', $patches);
-
-      // Handle patches-ignore -> ignore-dependency-patches
-      if (isset($extra['patches-ignore'])) {
-        $ignored = [];
-        foreach ($extra['patches-ignore'] as $package => $package_patches) {
-            // CP1 patches-ignore format is slightly different, but often it was just a list of patches.
-            // "patches-ignore": { "source/package": { "target/package": { "description": "url" } } }
-            // CP2 ignore-dependency-patches is just a list of packages whose patches should be ignored.
-            // "ignore-dependency-patches": ["some/package"]
-            $ignored[] = $package;
-        }
-        $composer_manipulator->removeSubNode('extra', 'patches-ignore');
-        $composer_manipulator->addSubNode('extra', 'composer-patches.ignore-dependency-patches', array_unique($ignored));
-      }
-
-      // Handle patchLevel -> package-depths
-      if (isset($extra['patchLevel'])) {
-        $depths = [];
-        foreach ($extra['patchLevel'] as $package => $level) {
-            // Convert -p1 to 1
-            $depths[$package] = (int) str_replace('-p', '', $level);
-        }
-        $composer_manipulator->removeSubNode('extra', 'patchLevel');
-        $composer_manipulator->addSubNode('extra', 'composer-patches.package-depths', $depths);
-      }
-
-      // Handle composer-exit-on-patch-failure -> exit-on-patch-failure
-      if (isset($extra['composer-exit-on-patch-failure'])) {
-        $composer_manipulator->removeSubNode('extra', 'composer-exit-on-patch-failure');
-        $composer_manipulator->addSubNode('extra', 'composer-patches.exit-on-patch-failure', $extra['composer-exit-on-patch-failure']);
-      }
-
-      // Handle composer-patches-skip-reporting -> skip-reporting
-      if (isset($extra['composer-patches-skip-reporting'])) {
-        $composer_manipulator->removeSubNode('extra', 'composer-patches-skip-reporting');
-        $composer_manipulator->addSubNode('extra', 'composer-patches.skip-reporting', $extra['composer-patches-skip-reporting']);
-      }
-
-      // Handle enable-patching (cleanup)
-      if (isset($extra['enable-patching'])) {
-        $composer_manipulator->removeSubNode('extra', 'enable-patching');
-      }
-
-      // Store the manipulated JSON file.
-      if (!file_put_contents($composer_filename, $composer_manipulator->getContents())) {
-        throw new \Exception('Composer file could not be saved.');
-      }
     }
     elseif ($patchType === self::PATCHTYPE_FILE_CP1) {
       $patches_filename = $extra['patches-file'];
@@ -98,28 +51,63 @@ protected function execute(InputInterface $input, OutputInterface $output): int
       // Update composer.json to use the new patches-file location.
       $composer_manipulator->removeSubNode('extra', 'patches-file');
       $composer_manipulator->addSubNode('extra', 'composer-patches.patches-file', $patches_filename);
-      
-      if (!file_put_contents($composer_filename, $composer_manipulator->getContents())) {
-        throw new \Exception('Composer file could not be saved.');
+    }
+
+    // Handle patches-ignore -> ignore-dependency-patches
+    if (isset($extra['patches-ignore'])) {
+      $ignored = [];
+      foreach ($extra['patches-ignore'] as $package => $package_patches) {
+        // CP1 patches-ignore format is slightly different, but often it was just a list of patches.
+        // "patches-ignore": { "source/package": { "target/package": { "description": "url" } } }
+        // CP2 ignore-dependency-patches is just a list of packages whose patches should be ignored.
+        // "ignore-dependency-patches": ["some/package"]
+        $ignored[] = $package;
+      }
+      $composer_manipulator->removeSubNode('extra', 'patches-ignore');
+      $composer_manipulator->addSubNode('extra', 'composer-patches.ignore-dependency-patches', array_unique($ignored));
+    }
+
+    // Handle patchLevel -> package-depths
+    if (isset($extra['patchLevel'])) {
+      $depths = [];
+      foreach ($extra['patchLevel'] as $package => $level) {
+        // Convert -p1 to 1
+        $depths[$package] = (int) str_replace('-p', '', $level);
       }
+      $composer_manipulator->removeSubNode('extra', 'patchLevel');
+      $composer_manipulator->addSubNode('extra', 'composer-patches.package-depths', $depths);
+    }
+
+    // Handle enable-patching, composer-patches-skip-reporting and composer-exit-on-patch-failure (cleanup)
+    $cleanup_keys = [
+      'enable-patching',
+      'composer-patches-skip-reporting',
+      'composer-exit-on-patch-failure',
+    ];
+    foreach ($cleanup_keys as $cleanup_key) {
+      if (isset($extra[$cleanup_key])) {
+        $composer_manipulator->removeSubNode('extra', $cleanup_key);
+      }
+    }
 
-      // Update the patches file itself.
-      $patches_file = new JsonFile($patches_filename);
-      $patches_manipulator = new JsonManipulator(file_get_contents($patches_file->getPath()));
-      // CP2 expects patches to be in the root "patches" key of the patches-file, which is the same as CP1.
-      // So no changes might be needed to the content of the file itself if it only contains "patches".
-      // However, we should check if there's anything else in there.
+    // Store the manipulated JSON file.
+    if (!file_put_contents($composer_filename, $composer_manipulator->getContents())) {
+      throw new \Exception('Composer file could not be saved.');
     }
 
     $output->writeln('Migration completed successfully.');
-    
-    $application = $this->getApplication();
-    $application->setAutoExit(FALSE);
+
+    $output->writeln(
+      '<info>Running composer update nothing to refresh lock file...</info>',
+    );
+    $this->updateLockFile();
+    $this->resetComposer();
+
     $output->writeln('<info>Relocking patches...</info>');
-    $application->run(new ArrayInput(['command' => 'patches-relock']), $output);
+    $this->runPatchesRelock();
 
     $output->writeln('<info>Repatching dependencies...</info>');
-    $application->run(new ArrayInput(['command' => 'patches-repatch']), $output);
+    $this->runRepatch();
 
     return 0;
   }
diff --git a/src/Composer/PatchMoveToLocalCommand.php b/src/Composer/PatchMoveToLocalCommand.php
index 783ff3d..1403b8c 100644
--- a/src/Composer/PatchMoveToLocalCommand.php
+++ b/src/Composer/PatchMoveToLocalCommand.php
@@ -147,14 +147,11 @@ protected function execute(
                 '<info>Remote Composer patches got successfully moved to local files and got updated in the composer.json or composer.patches.json.</info>'
             );
 
-            $application = $this->getApplication();
-            $application->setAutoExit(FALSE);
-
             if (!$this->isComposerPatches1()) {
                 $output->writeln('<info>Relocking patches...</info>');
-                $application->run(new ArrayInput(['command' => 'patches-relock']), $output);
+                $this->runPatchesRelock();
                 $output->writeln('<info>Repatching dependencies...</info>');
-                $application->run(new ArrayInput(['command' => 'patches-repatch']), $output);
+                $this->runRepatch();
             }
         } else {
             throw new \Exception(
diff --git a/src/Composer/PatchRemoveCommand.php b/src/Composer/PatchRemoveCommand.php
index a043641..05994f5 100644
--- a/src/Composer/PatchRemoveCommand.php
+++ b/src/Composer/PatchRemoveCommand.php
@@ -108,17 +108,15 @@ protected function execute(InputInterface $input, OutputInterface $output): int
     $output->writeln('The patch was successfully removed.');
 
     if (!$input->getOption('no-update')) {
-      $application = $this->getApplication();
-      $application->setAutoExit(FALSE);
-
+      $updateDevMode = !$input->hasOption('no-dev') || !$input->getOption('no-dev');
       if (!$this->isComposerPatches1()) {
         $output->writeln('<info>Relocking patches...</info>');
-        $application->run(new ArrayInput(['command' => 'patches-relock']), $output);
+        $this->runPatchesRelock();
         $output->writeln('<info>Repatching dependencies...</info>');
-        $application->run(new ArrayInput(['command' => 'patches-repatch']), $output);
+        $this->runRepatch();
       }
       $output->writeln('<info>Reinstalling package...</info>');
-      $application->run(new ArrayInput(['command' => 'reinstall', 'packages' => [$package]]), $output);
+      $this->runReinstall($package, $updateDevMode);
     }
 
     return 0;
diff --git a/src/Fixtures/composer.patches.json b/src/Fixtures/composer.patches.json
index 5fdab15..4b3fa6f 100644
--- a/src/Fixtures/composer.patches.json
+++ b/src/Fixtures/composer.patches.json
@@ -1,3 +1,3 @@
 {
   "patches": {}
-}
\ No newline at end of file
+}
diff --git a/tests/Fixtures/composer-migrate-root.json b/tests/Fixtures/composer-migrate-root.json
new file mode 100644
index 0000000..8490698
--- /dev/null
+++ b/tests/Fixtures/composer-migrate-root.json
@@ -0,0 +1,24 @@
+{
+    "name": "szeidler/composer-patches-cli-test",
+    "description": "Test package",
+    "require": {
+        "cweagans/composer-patches": "^2.0"
+    },
+    "extra": {
+        "composer-exit-on-patch-failure": true,
+        "patchLevel": {
+            "drupal/core": "-p2"
+        },
+        "enable-patching": true,
+        "patches": {
+            "vendor/package": {
+                "test patch": "test.patch"
+            }
+        }
+    },
+    "config": {
+        "allow-plugins": {
+            "cweagans/composer-patches": true
+        }
+    }
+}
diff --git a/tests/Fixtures/composer-migrate-root.lock b/tests/Fixtures/composer-migrate-root.lock
new file mode 100644
index 0000000..37d4d6c
--- /dev/null
+++ b/tests/Fixtures/composer-migrate-root.lock
@@ -0,0 +1,142 @@
+{
+    "_readme": [
+        "This file locks the dependencies of your project to a known state",
+        "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies",
+        "This file is @generated automatically"
+    ],
+    "content-hash": "de578f16f9dc9bdcc0a1b6b9f5d6fdd9",
+    "packages": [
+        {
+            "name": "cweagans/composer-configurable-plugin",
+            "version": "2.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/cweagans/composer-configurable-plugin.git",
+                "reference": "15433906511a108a1806710e988629fd24b89974"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/cweagans/composer-configurable-plugin/zipball/15433906511a108a1806710e988629fd24b89974",
+                "reference": "15433906511a108a1806710e988629fd24b89974",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=8.0.0"
+            },
+            "require-dev": {
+                "codeception/codeception": "~4.0",
+                "codeception/module-asserts": "^2.0",
+                "composer/composer": "~2.0",
+                "php-coveralls/php-coveralls": "~2.0",
+                "php-parallel-lint/php-parallel-lint": "^1.0.0",
+                "phpro/grumphp": "^1.8.0",
+                "sebastian/phpcpd": "^6.0",
+                "squizlabs/php_codesniffer": "^3.0"
+            },
+            "type": "library",
+            "autoload": {
+                "psr-4": {
+                    "cweagans\\Composer\\": "src"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Cameron Eagans",
+                    "email": "me@cweagans.net"
+                }
+            ],
+            "description": "Provides a lightweight configuration system for Composer plugins.",
+            "support": {
+                "issues": "https://github.com/cweagans/composer-configurable-plugin/issues",
+                "source": "https://github.com/cweagans/composer-configurable-plugin/tree/2.0.0"
+            },
+            "funding": [
+                {
+                    "url": "https://github.com/cweagans",
+                    "type": "github"
+                }
+            ],
+            "time": "2023-02-12T04:58:58+00:00"
+        },
+        {
+            "name": "cweagans/composer-patches",
+            "version": "2.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/cweagans/composer-patches.git",
+                "reference": "bfa6018a5f864653d9ed899b902ea72f858a2cf7"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/cweagans/composer-patches/zipball/bfa6018a5f864653d9ed899b902ea72f858a2cf7",
+                "reference": "bfa6018a5f864653d9ed899b902ea72f858a2cf7",
+                "shasum": ""
+            },
+            "require": {
+                "composer-plugin-api": "^2.0",
+                "cweagans/composer-configurable-plugin": "^2.0",
+                "ext-json": "*",
+                "php": ">=8.0.0"
+            },
+            "require-dev": {
+                "codeception/codeception": "~4.0",
+                "codeception/module-asserts": "^2.0",
+                "codeception/module-cli": "^2.0",
+                "codeception/module-filesystem": "^2.0",
+                "composer/composer": "~2.0",
+                "php-coveralls/php-coveralls": "~2.0",
+                "php-parallel-lint/php-parallel-lint": "^1.0.0",
+                "phpro/grumphp": "^1.8.0",
+                "sebastian/phpcpd": "^6.0",
+                "squizlabs/php_codesniffer": "^4.0"
+            },
+            "type": "composer-plugin",
+            "extra": {
+                "_": "The following two lines ensure that composer-patches is loaded as early as possible.",
+                "class": "cweagans\\Composer\\Plugin\\Patches",
+                "plugin-modifies-downloads": true,
+                "plugin-modifies-install-path": true
+            },
+            "autoload": {
+                "psr-4": {
+                    "cweagans\\Composer\\": "src"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Cameron Eagans",
+                    "email": "me@cweagans.net"
+                }
+            ],
+            "description": "Provides a way to patch Composer packages.",
+            "support": {
+                "issues": "https://github.com/cweagans/composer-patches/issues",
+                "source": "https://github.com/cweagans/composer-patches/tree/2.0.0"
+            },
+            "funding": [
+                {
+                    "url": "https://github.com/cweagans",
+                    "type": "github"
+                }
+            ],
+            "time": "2025-10-30T23:44:22+00:00"
+        }
+    ],
+    "packages-dev": [],
+    "aliases": [],
+    "minimum-stability": "stable",
+    "stability-flags": {},
+    "prefer-stable": false,
+    "prefer-lowest": false,
+    "platform": {},
+    "platform-dev": {},
+    "plugin-api-version": "2.9.0"
+}
diff --git a/tests/Fixtures/composer-pre-enable.json b/tests/Fixtures/composer-pre-enable.json
new file mode 100644
index 0000000..c16d82f
--- /dev/null
+++ b/tests/Fixtures/composer-pre-enable.json
@@ -0,0 +1,11 @@
+{
+  "name": "szeidler/composer-patches-cli-test-project",
+  "description": "Project for testing the extension.",
+  "type": "project",
+  "license": "MIT",
+  "config": {
+    "allow-plugins": {
+      "cweagans/composer-patches": true
+    }
+  }
+}
diff --git a/tests/PatchCommandTestBase.php b/tests/PatchCommandTestBase.php
index d7e5616..5f65449 100644
--- a/tests/PatchCommandTestBase.php
+++ b/tests/PatchCommandTestBase.php
@@ -4,6 +4,7 @@
 
 use Composer\Console\Application;
 use Composer\Factory;
+use Composer\IO\BufferIO;
 use Composer\IO\NullIO;
 use PHPUnit\Framework\TestCase;
 use Symfony\Component\Console\Tester\CommandTester;
@@ -41,7 +42,9 @@ protected function setUp(): void {
     $this->tempDir = sys_get_temp_dir() . '/composer-test-' . uniqid();
     mkdir($this->tempDir);
     $this->composerJsonPath = $this->tempDir . '/composer.json';
-    copy('tests/Fixtures/composer.json', $this->composerJsonPath);
+    if (file_exists('tests/Fixtures/composer.json')) {
+      copy('tests/Fixtures/composer.json', $this->composerJsonPath);
+    }
     chdir($this->tempDir);
   }
 
@@ -69,13 +72,57 @@ protected function recursiveRmdir(string $dir): void {
     rmdir($dir);
   }
 
+  /**
+   * Helper to create a dummy composer.lock file.
+   */
+  protected function createLockFile(array $packages = []) {
+    $packagesData = [];
+    foreach ($packages as $name => $version) {
+      if (is_int($name)) {
+        $name = $version;
+        $version = '1.0.0';
+      }
+      $packagesData[] = [
+        'name' => $name,
+        'version' => $version,
+        'source' => [
+          'type' => 'git',
+          'url' => 'https://example.com/' . $name . '.git',
+          'reference' => 'dummy',
+        ],
+        'dist' => [
+          'type' => 'zip',
+          'url' => 'https://example.com/' . $name . '.zip',
+          'reference' => 'dummy',
+          'shasum' => '',
+        ],
+        'type' => 'library',
+      ];
+    }
+
+    $lockData = [
+      '_readme' => ['This file is dummy.'],
+      'content-hash' => 'dummy',
+      'packages' => $packagesData,
+      'packages-dev' => [],
+      'aliases' => [],
+      'minimum-stability' => 'stable',
+      'stability-flags' => [],
+      'prefer-stable' => false,
+      'prefer-lowest' => false,
+      'platform' => [],
+      'platform-dev' => [],
+    ];
+    file_put_contents($this->tempDir . '/composer.lock', json_encode($lockData, JSON_PRETTY_PRINT));
+  }
+
   /**
    * Helper to create a CommandTester for a given command class.
    *
    * @return \Symfony\Component\Console\Tester\CommandTester
    */
   protected function getCommandTester(string $commandClass): CommandTester {
-    $io = new \Composer\IO\BufferIO();
+    $io = new BufferIO();
     $this->composer = Factory::create($io, $this->composerJsonPath, TRUE, TRUE);
     $application = new Application();
     $application->setAutoExit(FALSE);
diff --git a/tests/PatchEnableCommandTest.php b/tests/PatchEnableCommandTest.php
index 91b9fc0..0744110 100644
--- a/tests/PatchEnableCommandTest.php
+++ b/tests/PatchEnableCommandTest.php
@@ -14,6 +14,7 @@ class PatchEnableCommandTest extends PatchCommandTestBase {
    * Tests that patching is enabled in composer.json (Composer Patches 2 style).
    */
   public function testEnableComposerPatches2() {
+    copy(__DIR__ . '/Fixtures/composer-pre-enable.json', $this->composerJsonPath);
     // Ensure we start without patches
     $json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
     unset($json['extra']['composer-patches']['patches']);
@@ -39,6 +40,7 @@ public function testEnableComposerPatches2() {
    * Tests that patching is enabled in composer.json (Composer Patches 1 style).
    */
   public function testEnableComposerPatches1() {
+    copy(__DIR__ . '/Fixtures/composer-pre-enable.json', $this->composerJsonPath);
     // Mock Composer Patches 1 in requires
     $json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
     $json['require']['cweagans/composer-patches'] = '1.7.3';
@@ -62,6 +64,7 @@ public function testEnableComposerPatches1() {
    * Tests that patching is enabled with an external file.
    */
   public function testEnableWithExternalFile() {
+    copy(__DIR__ . '/Fixtures/composer-pre-enable.json', $this->composerJsonPath);
     $tester = $this->getCommandTester(PatchEnableCommand::class);
     $patchesFilename = 'patches.json';
 
@@ -85,6 +88,7 @@ public function testEnableWithExternalFile() {
    * Tests that patching is enabled with an external file (Composer Patches 1 style).
    */
   public function testEnableWithExternalFileComposerPatches1() {
+    copy(__DIR__ . '/Fixtures/composer-pre-enable.json', $this->composerJsonPath);
     // Mock Composer Patches 1 in requires
     $json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
     $json['require']['cweagans/composer-patches'] = '1.7.3';
@@ -113,6 +117,8 @@ public function testEnableWithExternalFileComposerPatches1() {
    * Tests that it fails if patches-file is already defined.
    */
   public function testEnableAlreadyDefined() {
+    copy(__DIR__ . '/Fixtures/composer-pre-enable.json', $this->composerJsonPath);
+
     $json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
     $json['extra']['composer-patches']['patches-file'] = 'existing.json';
     file_put_contents($this->composerJsonPath, json_encode($json));
diff --git a/tests/PatchMigrateCommandTest.php b/tests/PatchMigrateCommandTest.php
index df2e111..274a702 100644
--- a/tests/PatchMigrateCommandTest.php
+++ b/tests/PatchMigrateCommandTest.php
@@ -2,6 +2,9 @@
 
 namespace szeidler\ComposerPatchesCLI\Tests;
 
+use Composer\Factory;
+use Composer\IO\BufferIO;
+use cweagans\Composer\Plugin\Patches;
 use szeidler\ComposerPatchesCLI\Composer\PatchMigrateCommand;
 use szeidler\ComposerPatchesCLI\Exception\PatchMigrateConfigurationExistsException;
 use szeidler\ComposerPatchesCLI\Exception\PatchMigrateNoConfigurationFoundException;
@@ -11,35 +14,60 @@
  */
 class PatchMigrateCommandTest extends PatchCommandTestBase {
 
+  /**
+   * Helper to get a CommandTester with real CP2 commands.
+   */
+  protected function getMigrateCommandTester() {
+    $io = new BufferIO();
+    $this->composer = Factory::create($io, $this->composerJsonPath);
+    $application = new \Composer\Console\Application();
+    $application->setAutoExit(FALSE);
+    
+    // Register real CP2 commands and plugin if using Composer Patches 2.
+    if (class_exists('cweagans\Composer\Command\RelockCommand')) {
+      if (method_exists($application, 'addCommand')) {
+        $application->addCommand(new \cweagans\Composer\Command\RelockCommand());
+        $application->addCommand(new \cweagans\Composer\Command\RepatchCommand());
+      }
+      else {
+        $application->add(new \cweagans\Composer\Command\RelockCommand());
+        $application->add(new \cweagans\Composer\Command\RepatchCommand());
+      }
+
+      // Register the Patches plugin with the composer instance.
+      $plugin = new Patches();
+      $this->composer->getPluginManager()->addPlugin($plugin);
+    }
+
+    $command = new class extends PatchMigrateCommand {
+      protected function runRepatch(): void {
+        // Mock repatch to avoid full Installer run which requires real packages.
+        $this->getIO()->write('<info>Repatching dependencies...</info>');
+      }
+    };
+    $command->setComposer($this->composer);
+    $command->setIO($io);
+    $command->setApplication($application);
+
+    return new \Symfony\Component\Console\Tester\CommandTester($command);
+  }
+
+  /**
+   * Helper to create a dummy patch file.
+   */
+  protected function createDummyPatch(string $filename) {
+    file_put_contents($this->tempDir . '/' . $filename, "--- a/file\n+++ b/file\n@@ -1,1 +1,1 @@\n-old\n+new\n");
+  }
+
   /**
    * Tests migrating patches from the root composer.json.
    */
   public function testMigrateRoot() {
-    $composer_json = [
-      'name' => 'test/project',
-      'extra' => [
-        'patches' => [
-          'vendor/package' => [
-            'description' => 'https://example.com/patch.patch',
-          ],
-        ],
-        'patches-ignore' => [
-          'dependency/package' => [
-            'vendor/package' => [
-                'ignored patch' => 'https://example.com/ignored.patch'
-            ]
-          ],
-        ],
-        'patchLevel' => [
-          'vendor/package' => '-p2',
-        ],
-        'composer-exit-on-patch-failure' => true,
-        'enable-patching' => true,
-      ],
-    ];
-    file_put_contents($this->composerJsonPath, json_encode($composer_json, JSON_PRETTY_PRINT));
+    $this->createDummyPatch('test.patch');
+    copy(__DIR__ . '/Fixtures/composer-migrate-root.json', $this->composerJsonPath);
+    copy(__DIR__ . '/Fixtures/composer-migrate-root.lock', $this->tempDir . '/composer.lock');
 
-    $commandTester = $this->getCommandTester(PatchMigrateCommand::class);
+    $commandTester = $this->getMigrateCommandTester();
     $commandTester->execute([]);
 
     $this->assertStringContainsString('Migrating patches from root composer.json...', $commandTester->getDisplay());
@@ -48,32 +76,48 @@ public function testMigrateRoot() {
     $this->assertStringContainsString('Repatching dependencies...', $commandTester->getDisplay());
 
     $updated_composer_json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
-    
-    $this->assertArrayNotHasKey('patches', $updated_composer_json['extra']);
+
     $this->assertArrayHasKey('composer-patches', $updated_composer_json['extra']);
-    $this->assertEquals($composer_json['extra']['patches'], $updated_composer_json['extra']['composer-patches']['patches']);
-    
-    $this->assertArrayNotHasKey('patches-ignore', $updated_composer_json['extra']);
-    $this->assertEquals(['dependency/package'], $updated_composer_json['extra']['composer-patches']['ignore-dependency-patches']);
-    
+    $expected_patches = [
+      'vendor/package' => [
+        'test patch' => 'test.patch',
+      ],
+    ];
+    $this->assertEquals($expected_patches, $updated_composer_json['extra']['composer-patches']['patches']);
+    $this->assertArrayNotHasKey('patches', $updated_composer_json['extra']);
+
     $this->assertArrayNotHasKey('patchLevel', $updated_composer_json['extra']);
-    $this->assertEquals(['vendor/package' => 2], $updated_composer_json['extra']['composer-patches']['package-depths']);
-    
-    $this->assertArrayNotHasKey('composer-exit-on-patch-failure', $updated_composer_json['extra']);
-    $this->assertTrue($updated_composer_json['extra']['composer-patches']['exit-on-patch-failure']);
+    $this->assertEquals(['drupal/core' => 2], $updated_composer_json['extra']['composer-patches']['package-depths']);
 
     $this->assertArrayNotHasKey('enable-patching', $updated_composer_json['extra']);
+    $this->assertArrayNotHasKey('composer-exit-on-patch-failure', $updated_composer_json['extra']);
   }
 
   /**
    * Tests migrating patches from an external patches file.
    */
   public function testMigrateFile() {
+    $this->createDummyPatch('test.patch');
     $patches_file = 'patches.json';
     $composer_json = [
       'name' => 'test/project',
+      'require' => [
+        'cweagans/composer-patches' => '^2.0',
+      ],
       'extra' => [
         'patches-file' => $patches_file,
+        'patches-ignore' => [
+          'dependency/package' => [
+            'vendor/package' => [
+                'ignored patch' => 'https://example.com/ignored.patch'
+            ]
+          ],
+        ],
+        'patchLevel' => [
+          'vendor/package' => '-p2',
+        ],
+        'composer-patches-skip-reporting' => true,
+        'composer-exit-on-patch-failure' => true,
       ],
     ];
     file_put_contents($this->composerJsonPath, json_encode($composer_json, JSON_PRETTY_PRINT));
@@ -81,13 +125,14 @@ public function testMigrateFile() {
     $patches_json = [
       'patches' => [
         'vendor/package' => [
-          'description' => 'https://example.com/patch.patch',
+          'description' => 'test.patch',
         ],
       ],
     ];
     file_put_contents($this->tempDir . '/' . $patches_file, json_encode($patches_json, JSON_PRETTY_PRINT));
+    $this->createLockFile(['vendor/package' => '1.0.0']);
 
-    $commandTester = $this->getCommandTester(PatchMigrateCommand::class);
+    $commandTester = $this->getMigrateCommandTester();
     $commandTester->execute([]);
 
     $this->assertStringContainsString("Migrating patches from $patches_file...", $commandTester->getDisplay());
@@ -98,6 +143,15 @@ public function testMigrateFile() {
     $updated_composer_json = json_decode(file_get_contents($this->composerJsonPath), TRUE);
     $this->assertArrayNotHasKey('patches-file', $updated_composer_json['extra']);
     $this->assertEquals($patches_file, $updated_composer_json['extra']['composer-patches']['patches-file']);
+
+    $this->assertArrayNotHasKey('patches-ignore', $updated_composer_json['extra']);
+    $this->assertEquals(['dependency/package'], $updated_composer_json['extra']['composer-patches']['ignore-dependency-patches']);
+
+    $this->assertArrayNotHasKey('patchLevel', $updated_composer_json['extra']);
+    $this->assertEquals(['vendor/package' => 2], $updated_composer_json['extra']['composer-patches']['package-depths']);
+
+    $this->assertArrayNotHasKey('composer-patches-skip-reporting', $updated_composer_json['extra']);
+    $this->assertArrayNotHasKey('composer-exit-on-patch-failure', $updated_composer_json['extra']);
   }
 
   /**