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/Repository/Module/ModuleMigrationRepository.php

@@ -0,0 +1,75 @@
+<?php
+
+namespace MintyPHP\Repository\Module;
+
+use MintyPHP\DB;
+
+/**
+ * Manages the module_migrations tracking table.
+ *
+ * All SQL for module migration tracking lives here (strict layering).
+ */
+final class ModuleMigrationRepository implements ModuleMigrationRepositoryInterface
+{
+    public function ensureTrackingTable(): void
+    {
+        DB::query(
+            'CREATE TABLE IF NOT EXISTS `module_migrations` (
+                `id` INT UNSIGNED NOT NULL AUTO_INCREMENT,
+                `module_id` VARCHAR(64) NOT NULL,
+                `filename` VARCHAR(255) NOT NULL,
+                `applied_at` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+                PRIMARY KEY (`id`),
+                UNIQUE KEY `uq_module_migration` (`module_id`, `filename`)
+            ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci'
+        );
+    }
+
+    /**
+     * @return array<string, true> Filenames already applied, keyed by filename
+     */
+    public function getAppliedFilenames(string $moduleId): array
+    {
+        $applied = [];
+        $rows = DB::select('SELECT filename FROM module_migrations WHERE module_id = ?', $moduleId);
+        foreach ((array) $rows as $row) {
+            if (!is_array($row)) {
+                continue;
+            }
+            $filename = trim((string) (($row['module_migrations']['filename'] ?? $row['filename'] ?? '')));
+            if ($filename !== '') {
+                $applied[$filename] = true;
+            }
+        }
+        return $applied;
+    }
+
+    public function recordApplied(string $moduleId, string $filename): void
+    {
+        DB::query(
+            'INSERT INTO module_migrations (module_id, filename) VALUES (?, ?)',
+            $moduleId,
+            $filename
+        );
+    }
+
+    public function beginTransaction(): void
+    {
+        DB::query('START TRANSACTION');
+    }
+
+    public function commit(): void
+    {
+        DB::query('COMMIT');
+    }
+
+    public function rollback(): void
+    {
+        DB::query('ROLLBACK');
+    }
+
+    public function executeStatement(string $sql): void
+    {
+        DB::query($sql);
+    }
+}

core/Repository/Module/ModuleMigrationRepositoryInterface.php

@@ -0,0 +1,24 @@
+<?php
+
+namespace MintyPHP\Repository\Module;
+
+/** Contract for module migration tracking: table creation, applied-file queries, and statement execution. */
+interface ModuleMigrationRepositoryInterface
+{
+    public function ensureTrackingTable(): void;
+
+    /**
+     * @return array<string, true>
+     */
+    public function getAppliedFilenames(string $moduleId): array;
+
+    public function recordApplied(string $moduleId, string $filename): void;
+
+    public function beginTransaction(): void;
+
+    public function commit(): void;
+
+    public function rollback(): void;
+
+    public function executeStatement(string $sql): void;
+}