refactor: rename lib/ to core/ for clearer core-module separation

Rename the top-level lib/ directory to core/ so the project root
immediately communicates which code is core platform and which lives
in modules/. PHP namespaces (MintyPHP\*) are unchanged — only the
Composer PSR-4 path mapping moves from lib/ to core/.

Module-internal lib/ directories (modules/*/lib/) are untouched.

Updated across the full stack:
- composer.json PSR-4 mapping
- bootstrap entry points (web/index.php, bin/*, tests/bootstrap.php)
- tooling configs (phpstan.neon, phpunit.xml, php-cs-fixer)
- 26 architecture contract tests
- enforcement-policy, guard-catalog, quality-gates
- all documentation (CLAUDE.md, README, 25 docs/, .agents/skills/)
- bin/qa-extended.sh search paths
- .claude/settings.local.json permission paths

Workflow: .agents/runs/CORE-LIB-RENAME-001/ (Analyst → Planner →
Executor → Code Review (4 findings fixed) → Security Review →
Acceptance Test → Finalizer)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

core/Service/Module/ModuleMigrationService.php

@@ -0,0 +1,98 @@
+<?php
+
+namespace MintyPHP\Service\Module;
+
+use MintyPHP\App\Module\ModuleRegistry;
+use MintyPHP\Repository\Module\ModuleMigrationRepository;
+use MintyPHP\Support\SqlStatementParser;
+use RuntimeException;
+
+/**
+ * Discovers and applies pending SQL migrations for all enabled modules.
+ *
+ * Orchestration only — SQL lives in ModuleMigrationRepository,
+ * statement parsing in SqlStatementParser.
+ */
+final class ModuleMigrationService
+{
+    public function __construct(
+        private readonly ModuleRegistry $registry,
+        private readonly ModuleMigrationRepository $repository,
+    ) {
+    }
+
+    /**
+     * Apply all pending module migrations.
+     *
+     * @return array{ok: bool, applied: int, skipped_empty: int, modules_enabled: int}
+     */
+    public function applyPendingMigrations(): array
+    {
+        $modules = $this->registry->getModules();
+        $modulesEnabled = count($modules);
+
+        if ($modulesEnabled === 0) {
+            return ['ok' => true, 'applied' => 0, 'skipped_empty' => 0, 'modules_enabled' => 0];
+        }
+
+        $this->repository->ensureTrackingTable();
+
+        $totalApplied = 0;
+        $skippedEmpty = 0;
+
+        foreach ($modules as $manifest) {
+            $migrationsPath = $manifest->migrationsPath;
+            if ($migrationsPath === null || !is_dir($migrationsPath)) {
+                continue;
+            }
+
+            $files = glob($migrationsPath . '/*.sql');
+            if ($files === false || count($files) === 0) {
+                continue;
+            }
+            sort($files);
+
+            $applied = $this->repository->getAppliedFilenames((string) $manifest->id);
+
+            foreach ($files as $file) {
+                $filename = basename($file);
+                if (isset($applied[$filename])) {
+                    continue;
+                }
+
+                $sql = file_get_contents($file);
+                if ($sql === false || trim($sql) === '') {
+                    $skippedEmpty++;
+                    continue;
+                }
+
+                $this->repository->beginTransaction();
+                try {
+                    $statements = SqlStatementParser::splitStatements($sql);
+                    foreach ($statements as $statement) {
+                        $this->repository->executeStatement($statement);
+                    }
+
+                    $this->repository->recordApplied((string) $manifest->id, $filename);
+                    $this->repository->commit();
+                } catch (\Throwable $migrationError) {
+                    $this->repository->rollback();
+                    throw new RuntimeException(
+                        sprintf("Migration %s/%s failed: %s", $manifest->id, $filename, $migrationError->getMessage()),
+                        0,
+                        $migrationError
+                    );
+                }
+
+                $totalApplied++;
+            }
+        }
+
+        return [
+            'ok' => true,
+            'applied' => $totalApplied,
+            'skipped_empty' => $skippedEmpty,
+            'modules_enabled' => $modulesEnabled,
+        ];
+    }
+}