refactor: extract shared code from bin/ scripts and remove legacy scheduler runner

- Extract ModuleManifestLoader for standalone manifest loading (used by
  module-deactivate and ValidateCommand)
- Extract SqlStatementParser, ModuleMigrationRepository, and
  ModuleMigrationService from bin/module-migrate.php to enforce strict
  layering (SQL in repository, orchestration in service)
- Delete bin/scheduler-run.php (fully superseded by bin/console scheduler:run)
- Update docs and test fixtures to reference bin/console

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

lib/App/Module/ModuleManifestLoader.php

@@ -0,0 +1,42 @@
+<?php
+
+namespace MintyPHP\App\Module;
+
+use RuntimeException;
+
+/**
+ * Loads a single module manifest from disk without requiring the module to be enabled.
+ *
+ * Unlike ModuleRegistry (which only loads enabled modules), this loader can resolve
+ * any module by its directory — used by validation and deactivation tooling.
+ */
+final class ModuleManifestLoader
+{
+    /**
+     * Load and validate a module manifest from its on-disk location.
+     *
+     * @param string $modulesDir Absolute path to the modules/ directory
+     * @param string $moduleId   Directory name / module ID
+     *
+     * @throws RuntimeException If the manifest file is missing or invalid
+     */
+    public static function loadFromDisk(string $modulesDir, string $moduleId): ModuleManifest
+    {
+        $manifestFile = rtrim($modulesDir, '/') . '/' . $moduleId . '/module.php';
+
+        if (!is_file($manifestFile)) {
+            throw new RuntimeException(
+                "Module manifest not found at: {$manifestFile}"
+            );
+        }
+
+        $raw = require $manifestFile;
+        if (!is_array($raw)) {
+            throw new RuntimeException(
+                "Module manifest at '{$manifestFile}' must return an array."
+            );
+        }
+
+        return ModuleManifest::fromArray($raw, dirname($manifestFile));
+    }
+}