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/Settings/SettingRepository.php

@@ -0,0 +1,36 @@
+<?php
+
+namespace MintyPHP\Repository\Settings;
+
+use MintyPHP\DB;
+
+/** Reads and upserts application settings as key-value pairs in the database. */
+class SettingRepository implements SettingRepositoryInterface
+{
+    public function find(string $key): ?array
+    {
+        $row = DB::selectOne('select `key`, `value`, `description`, `updated_at` from settings where `key` = ? limit 1', $key);
+        if (!$row) {
+            return null;
+        }
+        return $row['settings'] ?? $row;
+    }
+
+    public function getValue(string $key): ?string
+    {
+        $row = $this->find($key);
+        if (!$row) {
+            return null;
+        }
+        return array_key_exists('value', $row) ? (string) $row['value'] : null;
+    }
+
+    public function set(string $key, ?string $value, ?string $description = null): bool
+    {
+        $query = 'insert into settings (`key`, `value`, `description`) values (?, ?, ?) '
+            . 'on duplicate key update `value` = values(`value`), '
+            . '`description` = ifnull(values(`description`), `description`)';
+        $result = DB::update($query, $key, $value, $description);
+        return $result !== false;
+    }
+}