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.

config/packages/doctrine.yaml

@@ -28,12 +28,6 @@ doctrine:
             App\Shared\Domain\Contract\ClientInterface: App\Module\Directory\Domain\Entity\Client
             App\Shared\Domain\Contract\ClientTicketInterface: App\Module\ClientPortal\Domain\Entity\ClientTicket
         mappings:
-            App:
-                type: attribute
-                is_bundle: false
-                dir: '%kernel.project_dir%/src/Entity'
-                prefix: 'App\Entity'
-                alias: App
             Core:
                 type: attribute
                 is_bundle: false