refactor(core) : final legacy cleanup — app is 100% modular

LST-60 (3.3). Closes the modular-monolith migration. src/Entity was already
empty; this removes the last legacy residue.

- Doctrine: drop the legacy "App" mapping (empty src/Entity). resolve_target_
  entities already targets modules only.
- MCP User tools (Reference/) -> Core/Infrastructure/Mcp/Tool; MCP Serializer
  -> Shared/Infrastructure/Mcp (33 usages repointed).
- Controllers (mark-all-read, notification unread-count, regenerate-api-token,
  user-avatar) -> Core/Infrastructure/Controller. TokenEncryptor -> Shared/
  Infrastructure/Service (11 usages). AppVersion resource+provider -> Shared.
  ContractType enum -> Core/Domain/Enum.
- src/{Entity,State,Controller,Service,Enum,ApiResource} now empty; routes,
  MCP tool names and public API unchanged.

180 tests green, mapping valid, no route regression, cs-fixer clean.
Note: final Malio visual harmonisation (subjective) left to the PO.

src/Module/Integration/Infrastructure/ApiPlatform/State/GiteaSettingsProcessor.php

@@ -9,7 +9,7 @@ use ApiPlatform\State\ProcessorInterface;
 use App\Module\Integration\Domain\Entity\GiteaConfiguration;
 use App\Module\Integration\Domain\Repository\GiteaConfigurationRepositoryInterface;
 use App\Module\Integration\Infrastructure\ApiPlatform\Resource\GiteaSettings;
-use App\Service\TokenEncryptor;
+use App\Shared\Infrastructure\Service\TokenEncryptor;
 use Doctrine\ORM\EntityManagerInterface;
 
 final readonly class GiteaSettingsProcessor implements ProcessorInterface