Issue 11: Remove deprecated artifact entities and repositories

[adamhjk]

Clean up the codebase by removing old artifact entities and repositories after migration is complete.

Key Changes

• Delete old entity files:
  • src/domain/models/model_input.ts
  • src/domain/models/model_resource.ts
  • src/domain/models/model_data.ts
  • src/domain/models/model_file.ts
  • src/domain/models/model_log.ts
• Delete old repository files:
  • src/infrastructure/persistence/yaml_input_repository.ts
  • src/infrastructure/persistence/yaml_resource_repository.ts
  • src/infrastructure/persistence/yaml_data_repository.ts
  • src/infrastructure/persistence/file_system_file_repository.ts
  • src/infrastructure/persistence/streaming_log_repository.ts
• Update src/domain/models/repositories.ts:
  • Remove: InputRepository, ResourceRepository, DataRepository, FileRepository, LogRepository interfaces
  • Keep: OutputRepository (updated in Issue Issue 3: Update ModelOutput to reference unified Data #118)
• Remove old repository factories from repository_factory.ts
• Update all imports throughout codebase

Acceptance Criteria

• All old artifact files deleted
• All old repository files deleted
• No references to old entities in codebase
• All tests passing
• deno check passes (no type errors)
• deno lint passes

Dependencies

• Issue Issue 7: Migrate remaining models to new architecture #122 (All models migrated)
• Issue Issue 8: Update CLI commands for new architecture #123 (All CLI commands updated)
• Issue Issue 10: Create data migration tool #125 (Migration tool available for any stragglers)

Files to Delete

• src/domain/models/model_input.ts
• src/domain/models/model_resource.ts
• src/domain/models/model_data.ts
• src/domain/models/model_file.ts
• src/domain/models/model_log.ts
• src/infrastructure/persistence/yaml_input_repository.ts
• src/infrastructure/persistence/yaml_resource_repository.ts
• src/infrastructure/persistence/yaml_data_repository.ts
• src/infrastructure/persistence/file_system_file_repository.ts
• src/infrastructure/persistence/streaming_log_repository.ts

Files to Update

• src/domain/models/repositories.ts
• src/infrastructure/persistence/repository_factory.ts
• All files with imports from deleted files