fix(repository): resolve remaining late-binding hazards from the audit

Three fixes for the ComposerRepository/FilesystemRepository/PlatformRepository
hazards where inner-composition delegation skipped PHP's late-bound virtual
dispatch:

- ComposerRepository::has_package now builds its packageMap through the
  late-bound getPackages() equivalent, so lazy-providers repos surface the
  LogicException and available-packages repos load their package list, as in
  PHP, instead of silently answering false from the raw array.

- RepositoryInterface::get_repo_name returns anyhow::Result<String>: PHP's
  getRepoName() counts through the late-bound initialize(), which is fallible
  in file-reading subclasses. FilesystemRepository and PackageRepository now
  run that initialization instead of freezing the inner array repository to an
  empty state (which also made a later write() truncate installed.json).
  Supporting changes keep the initialization chain callable from &self:
  JsonFile::read takes &self (indent moved into a RefCell), FilesystemRepository
  dev_mode became a Cell, and WritableArrayRepository dev_package_names a
  RefCell.

- PlatformRepository::new routes constructor packages through its own
  add_package so the override handling and full platform initialization run
  as they do via PHP's parent constructor; the inner find_package/add_package
  delegations inside add_package (and ComposerRepository::add_package) gained
  the same is_initialized guard, since the constructor path would otherwise
  freeze the repository.

Same defect class as 7db937af, 97b5211a and 3e367f78.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

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