diff --git a/.cspell.json b/.cspell.json
index 368b755a17868f53cf92edf4323b51355b976da7..950ad4ab51bff4676f5004a090da2bee34caae75 100644
--- a/.cspell.json
+++ b/.cspell.json
@@ -4,7 +4,6 @@
     { "name": "automatic_updates", "path": "./dictionary.txt"}
   ],
   "ignorePaths": [
-    "pcre.ini",
     "README.md"
   ]
 }
diff --git a/automatic_updates_extensions/tests/src/Functional/UpdaterFormTestBase.php b/automatic_updates_extensions/tests/src/Functional/UpdaterFormTestBase.php
index a154b524420d170cb31b5902156ba21e5aa58e21..061781f28838e376a78a05a1b3641b819bc4b804 100644
--- a/automatic_updates_extensions/tests/src/Functional/UpdaterFormTestBase.php
+++ b/automatic_updates_extensions/tests/src/Functional/UpdaterFormTestBase.php
@@ -46,19 +46,16 @@ abstract class UpdaterFormTestBase extends UpdaterFormFunctionalTestBase {
         'name' => 'drupal/semver_test',
         'version' => '8.1.0',
         'type' => 'drupal-module',
-        'install_path' => '../../web/projects/semver_test',
       ])
       ->addPackage([
         'name' => 'drupal/aaa_update_test',
         'version' => '2.0.0',
         'type' => 'drupal-module',
-        'install_path' => '../../web/projects/aaa_update_test',
       ])
       ->addPackage([
         'name' => 'drupal/automatic_updates_extensions_test_theme',
         'version' => '2.0.0',
         'type' => 'drupal-theme',
-        'install_path' => '../../web/projects/automatic_updates_extensions_test_theme',
       ])
       ->commitChanges();
     $this->drupalPlaceBlock('local_tasks_block', ['primary' => TRUE]);
diff --git a/drupalci.yml b/drupalci.yml
index 422d14d781e7aa035d8e2e450ae2dc060d8653aa..2d5633337e734fff426a10ffd58847e12393b7ee 100644
--- a/drupalci.yml
+++ b/drupalci.yml
@@ -9,12 +9,6 @@ build:
       # Run code quality checks.
       container_command.commit-checks:
         commands:
-          # Disable the PCRE engine's JIT, since it causes Composer to die during the
-          # update process, but only on Drupal CI, and for reasons that are essentially
-          # impossible to trace into. The PCRE JIT is not necessary for Automatic Updates
-          # to work correctly, and disabling it is a known workaround.
-          # @see pcre.ini
-          - sudo cp modules/contrib/automatic_updates/pcre.ini /usr/local/etc/php/conf.d
           # @todo Replace in favor of commit-code-check.sh once https://www.drupal.org/project/drupal/issues/3314100 lands.
           - modules/contrib/automatic_updates/scripts/commit-code-check.sh --drupalci
         halt-on-fail: true
diff --git a/package_manager/tests/modules/fixture_manipulator/src/FixtureManipulator.php b/package_manager/tests/modules/fixture_manipulator/src/FixtureManipulator.php
index a333efff4d6248e42e4faca5a51d28534eb2e8bf..b08421244e8db636418e6b1b8d7dd923e13944dd 100644
--- a/package_manager/tests/modules/fixture_manipulator/src/FixtureManipulator.php
+++ b/package_manager/tests/modules/fixture_manipulator/src/FixtureManipulator.php
@@ -11,7 +11,14 @@ use Symfony\Component\Filesystem\Filesystem as SymfonyFileSystem;
 use Drupal\Component\Serialization\Yaml;
 
 /**
- * It manipulates.
+ * Manipulates a test fixture using Composer commands.
+ *
+ * The composer.json file CANNOT be safely created or modified using the
+ * json_encode() function, because Composer does not use a real JSON parser — it
+ * updates composer.json using \Composer\Json\JsonManipulator, which is known to
+ * choke in a number of scenarios.
+ *
+ * @see https://www.drupal.org/i/3346628
  */
 class FixtureManipulator {
 
@@ -563,6 +570,46 @@ class FixtureManipulator {
     return $plain_output;
   }
 
+  /**
+   * Transform the received $package into options for `composer init`.
+   *
+   * @param array $package
+   *   A Composer package definition.
+   *
+   * @return array
+   *   The corresponding `composer init` options.
+   */
+  private static function getComposerInitOptionsForPackage(array $package): array {
+    return array_filter(array_map(function ($k, $v) {
+      switch ($k) {
+        case 'name':
+        case 'description':
+        case 'type':
+          return "--$k=$v";
+
+        case 'require':
+        case 'require-dev':
+          $requirements = array_map(
+            fn(string $req_package, string $req_version): string => "$req_package:$req_version",
+            array_keys($v),
+            array_values($v)
+          );
+          return "--$k=" . implode(',', $requirements);
+
+        case 'version':
+          // This gets set in the repository metadata itself.
+          return NULL;
+
+        case 'extra':
+          // Cannot be set using `composer init`, only `composer config` can.
+          return NULL;
+
+        default:
+          throw new \InvalidArgumentException($k);
+      }
+    }, array_keys($package), array_values($package)));
+  }
+
   /**
    * Adds a path repository.
    *
@@ -576,30 +623,39 @@ class FixtureManipulator {
     $name = $package['name'];
     $path_repo_base = \Drupal::state()->get(self::PATH_REPO_STATE_KEY);
     $repo_path = "$path_repo_base/" . str_replace('/', '--', $name);
-    $composer_json_path = $repo_path . DIRECTORY_SEPARATOR . 'composer.json';
     $fs = new SymfonyFileSystem();
     if (!is_dir($repo_path)) {
       // Create the repo if it does not exist.
       $fs->mkdir($repo_path);
-      file_put_contents($composer_json_path, json_encode($package, JSON_THROW_ON_ERROR));
-      $repository = json_encode([
-        'type' => 'path',
-        'url' => $repo_path,
-        'options' => [
-          'symlink' => FALSE,
-        ],
-      ], JSON_UNESCAPED_SLASHES);
-      $this->runComposerCommand(['config', "repo.$name", $repository]);
-    }
-    else {
-      $composer_json_data = json_decode(file_get_contents($composer_json_path), TRUE);
-      // Update the version if needed.
-      // @todo Should we create 1 repo per version.
-      if ($composer_json_data['version'] !== $package['version']) {
-        $composer_json_data['version'] = $package['version'];
-        file_put_contents($composer_json_path, json_encode($composer_json_data, JSON_THROW_ON_ERROR));
+      // Switch the working directory from project root to repo path.
+      $project_root_dir = $this->dir;
+      $this->dir = $repo_path;
+      // Create a composer.json file using `composer init`.
+      $this->runComposerCommand(['init', ...static::getComposerInitOptionsForPackage($package)]);
+      // Set the `extra` property in the generated composer.json file using
+      // `composer config`, because `composer init` does not support it.
+      foreach ($package['extra'] ?? [] as $extra_property => $extra_value) {
+        $this->runComposerCommand(['config', "extra.$extra_property", '--json', json_encode($extra_value, JSON_UNESCAPED_SLASHES)]);
       }
-    }
+      // Restore the project root as the working directory.
+      $this->dir = $project_root_dir;
+    }
+
+    // Register the repository, keyed by package name. This ensures each package
+    // is registered only once and its version can be updated.
+    // @todo Should we create 1 repo per version.
+    $repository = json_encode([
+      'type' => 'path',
+      'url' => $repo_path,
+      'options' => [
+        'symlink' => FALSE,
+        'versions' => [
+          $name => $package['version'],
+        ],
+      ],
+    ], JSON_UNESCAPED_SLASHES);
+    $this->runComposerCommand(['config', "repo.$name", $repository]);
+
     return $repo_path;
   }
 
@@ -627,17 +683,8 @@ class FixtureManipulator {
     }
     // Update all the repos in the composer.json file to point to the new
     // repos at the absolute path.
-    $json_data = json_decode(file_get_contents($this->dir . '/composer.json'), TRUE);
-    $composer_json_needs_update = FALSE;
-    foreach ($json_data['repositories'] as &$existing_repo_data) {
-      if (is_array($existing_repo_data) && isset($existing_repo_data['url']) && str_starts_with($existing_repo_data['url'], '../path_repos/')) {
-        $composer_json_needs_update = TRUE;
-        $existing_repo_data['url'] = str_replace('../path_repos/', "$path_repo_base/", $existing_repo_data['url']);
-      }
-    }
-    if ($composer_json_needs_update) {
-      file_put_contents($this->dir . '/composer.json', json_encode($json_data, JSON_THROW_ON_ERROR));
-    }
+    $composer_json = file_get_contents($this->dir . '/composer.json');
+    file_put_contents($this->dir . '/composer.json', str_replace('../path_repos/', "$path_repo_base/", $composer_json));
     $this->runComposerCommand(['install']);
   }
 
diff --git a/pcre.ini b/pcre.ini
deleted file mode 100644
index 0c5780afafe9b255bf7bb317c8c030b13fa4f740..0000000000000000000000000000000000000000
--- a/pcre.ini
+++ /dev/null
@@ -1,8 +0,0 @@
-# This file is used on Drupal CI because Composer occasionally dies with
-# PCRE_JIT_STACKLIMIT_ERROR during certain test cases, and there is no insight
-# into where the failure is happening, or why. This has only been observed on
-# Drupal CI. Since the PCRE engine's JIT is not strictly necessary to the
-# functioning of the Automatic Updates module, this file disables the PCRE JIT
-# as a workaround.
-# @see drupalci.yml
-pcre.jit = 0
diff --git a/scripts/src/Converter.php b/scripts/src/Converter.php
index 0bdb88655af16fc89b529736bd91a37d15975531..36fbc8f872435245603594c93509cd6c21be9fea 100644
--- a/scripts/src/Converter.php
+++ b/scripts/src/Converter.php
@@ -72,7 +72,6 @@ class Converter {
       'drupalci.yml',
       'README.md',
       '.git',
-      'pcre.ini',
       'composer.json',
       '.gitattributes',
       '.gitignore',