Issue #83: enforce document-only input.write snapshot contract

[AmirTlinov]

Summary

• cut input.write over to full-replace document payloads (+ validate_only)
• removed public op/granular write contract from schema, parser, tests, and docs
• kept finalize checks fail-closed for normal + validate-only write paths

Validation

• cargo fmt --check
• cargo clippy --all-targets --all-features -- -D warnings
• cargo test --all-targets --all-features
• scripts/check_coverage_baseline.sh
• cargo audit

Refs #83

[AmirTlinov]

@review review

[AmirTlinov]

VERDICT: PASS

Scope-only review for issue #83 is satisfied.

• input.write is document-only full-replace snapshot (document) and op/legacy granular mutations are rejected with actionable guidance (schema + parser + tests).
• validate_only performs finalize checks without persistence (no revision/state mutation).
• Fail-closed finalize validation is preserved for both draft and finalize paths.
• No scope drift: only README.md, src/adapters/mcp_stdio/mod.rs, src/adapters/mcp_stdio/schema.rs, src/adapters/mcp_stdio/tool_input.rs, src/app/input_usecases.rs, src/domain/models.rs, tests/e2e.rs, tests/integration_test.rs changed.
• Verification: cargo test --all-targets --all-features, cargo test --test e2e, cargo test --test integration_test

Context pack: https://chat.openai.com/c/PK_NOT_SUPPORTED? Actually this is placeholder?

[AmirTlinov]

VERDICT: PASS\n\nPASS with no blocking findings.\n- Document-only contract and validate-only dry-run are implemented and tested.\n- Legacy /mutation field writes return clear migration guidance.\n- Finalize fail-closed checks remain enforced on write paths.\n\nVerification artifacts: unit/adapter/e2e/integration tests all passing on PR branch (

running 83 tests
test adapters::mcp_stdio::tool_output::tests::default_output_read_uses_orchestrator_profile ... ok
test adapters::mcp_stdio::tests::test_output_format_parameter_is_rejected ... ok
test adapters::mcp_stdio::tests::test_parse_initialize_timeout_ms ... ok
test adapters::mcp_stdio::tool_output::tests::explicit_profile_is_parsed ... ok
test adapters::mcp_stdio::tool_output::tests::page_token_is_forwarded_without_profile_override ... ok
test adapters::mcp_stdio::tool_output::tests::legacy_read_fields_are_rejected ... ok
test adapters::mcp_stdio::tests::test_domain_error_contract_for_migration_required ... ok
test adapters::mcp_stdio::tests::test_domain_error_contract_for_pack_id_conflict ... ok
test adapters::mcp_stdio::tests::test_domain_error_contract_for_deserialize_error ... ok
test adapters::mcp_stdio::tests::test_domain_error_contract_is_strict_json ... ok
test adapters::mcp_stdio::tests::test_domain_error_contract_keeps_string_request_id ... ok
test adapters::storage_json::tests::test_decode_rejects_malformed ... ok
test adapters::mcp_stdio::tool_output::tests::selected_metadata_remains_present_when_content_contains_marker_substrings ... ok
test adapters::mcp_stdio::tool_output::tests::selected_metadata_is_deterministically_overwritten_in_legend ... ok
test adapters::storage_json::tests::test_encode_decode_roundtrip ... ok
test adapters::storage_json::tests::test_decode_with_path_wraps_migration_error ... ok
test adapters::storage_json::tests::test_list_pack_paths_nonexistent_dir ... ok
test adapters::mcp_stdio::tests::test_frame_size_limit ... ok
test adapters::mcp_stdio::tests::test_oversized_header_line_is_rejected ... ok
test adapters::mcp_stdio::tests::test_content_length_header_case_insensitive ... ok
test adapters::mcp_stdio::tests::test_oversized_json_line_is_rejected ... ok
test adapters::mcp_stdio::tests::test_content_type_then_content_length_is_accepted ... ok
test adapters::mcp_stdio::tests::test_json_line_batch_messages_are_parsed_sequentially ... ok
test adapters::mcp_stdio::tests::test_content_length_framing ... ok
test adapters::mcp_stdio::tests::test_plain_json_line_is_accepted ... ok
test adapters::mcp_stdio::tests::test_plain_json_without_newline_is_accepted ... ok
test adapters::mcp_stdio::tests::test_plain_multiline_json_is_rejected ... ok
test adapters::mcp_stdio::tests::test_transport_mode_detection ... ok
test adapters::storage_json::tests::test_load_all_active_skips_and_removes_corrupt_or_oversized_pack ... ok
test app::ports::tests::freshness_state_boundaries_are_stable ... ok
test adapters::storage_json::tests::test_purge_expired_removes_only_expired ... ok
test app::resolver::tests::resolve_by_id_success ... ok
test adapters::storage_json::tests::test_write_pack_atomic_persists_and_is_decodable ... ok
test app::resolver::tests::resolve_by_id_not_found_no_name_fallthrough ... ok
test app::resolver::tests::resolve_empty_identifier_returns_invalid_data ... ok
test adapters::code_excerpt_fs::tests::test_file_not_found_returns_stale_ref ... ok
test adapters::storage_json::tests::test_get_by_id_returns_none_for_corrupt_pack_and_recovers_file ... ok
test domain::models::tests::test_cannot_finalize_empty_pack ... ok
test app::resolver::tests::resolve_by_name_success ... ok
test adapters::storage_json::tests::test_purge_expired_removes_unreadable_and_oversized_pack_files ... ok
test domain::models::tests::test_extend_ttl_from_now_when_already_expired ... ok
test adapters::storage_json::tests::test_load_all_active_excludes_expired ... ok
test adapters::code_excerpt_fs::tests::test_path_outside_root_is_rejected ... ok
test adapters::code_excerpt_fs::tests::test_file_too_large_is_rejected ... ok
test adapters::code_excerpt_fs::tests::test_range_end_exceeds_total_lines ... ok
test adapters::code_excerpt_fs::tests::test_reads_exact_lines ... ok
test app::resolver::tests::resolve_name_not_found ... ok
test adapters::code_excerpt_fs::tests::test_crlf_line_endings_are_trimmed ... ok
test domain::models::tests::test_is_expired_when_future ... ok
test domain::models::tests::test_is_expired_when_past ... ok
test adapters::code_excerpt_fs::tests::test_reads_single_line ... ok
test domain::models::tests::test_migrate_schema_ahead_returns_error ... ok
test adapters::storage_json::tests::test_save_with_expected_revision_rejects_oversized_payload_with_validation_error ... ok
test adapters::storage_json::tests::test_create_new_rejects_oversized_payload_with_validation_error ... ok
test adapters::storage_json::tests::test_delete_pack_file_removes_target_without_reading_payload ... ok
test domain::models::tests::test_migrate_schema_rejects_non_compact_pack_id ... ok
test domain::models::tests::test_cannot_finalize_with_only_empty_section ... ok
test domain::models::tests::test_set_ttl_and_extend_ttl ... ok
test domain::models::tests::test_ttl_must_be_positive ... ok
test domain::models::tests::test_finalize_minimal_pack_succeeds ... ok
test adapters::storage_json::tests::test_get_by_name_prefers_latest_finalized_then_revision ... ok
test domain::models::tests::test_migrate_schema_rejects_older_schema ... ok
test domain::models::tests::test_set_meta_requires_fields ... ok
test adapters::storage_json::tests::test_get_by_name_reports_candidate_ids_on_rank_tie ... ok
test domain::models::tests::test_delete_ref_not_found_returns_error ... ok
test domain::models::tests::test_revision_increments_on_mutation ... ok
test domain::models::tests::test_cannot_finalize_without_qa_verdict ... ok
test domain::models::tests::test_finalized_pack_is_immutable ... ok
test domain::models::tests::test_ttl_remaining_human_expired ... ok
test domain::models::tests::test_ttl_remaining_human_hours ... ok
test domain::models::tests::test_ttl_remaining_human_minutes ... ok
test adapters::storage_json::tests::test_list_packs_filters_by_freshness_and_can_surface_expired ... ok
test domain::types::tests::test_line_range_span_limit ... ok
test domain::types::tests::test_line_range_validation ... ok
test domain::types::tests::test_pack_name_must_not_look_like_pack_id ... ok
test domain::types::tests::test_pack_name_validation ... ok
test domain::types::tests::test_pack_id_validation ... ok
test domain::types::tests::test_relative_path_validation ... ok
test domain::types::tests::test_status_from_str ... ok
test domain::models::tests::test_upsert_ref_replaces_existing ... ok
test domain::types::tests::test_section_key_validation ... ok
test adapters::code_excerpt_fs::tests::test_range_start_exceeds_total_lines ... ok
test adapters::mcp_stdio::tests::test_tool_success_rejects_oversized_payload ... ok

test result: ok. 83 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.18s

running 0 tests

test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s

running 25 tests
test e2e_v3_rejects_legacy_actions_with_invalid_data ... ok
test e2e_server_exits_if_initialize_never_arrives ... ok
test e2e_initialize_accepts_unframed_json_message ... ok
test e2e_output_rejects_format_parameter ... ok
test e2e_initialize_with_content_type_header ... ok
test e2e_unframed_json_line_batch_is_processed_sequentially ... ok
test e2e_touch_ttl_requires_mode_field ... ok
test e2e_notification_without_id_produces_no_response ... ok
test e2e_create_requires_ttl_minutes ... ok
test e2e_input_rejects_legacy_alias_fields ... ok
test e2e_schema_mismatch_reports_migration_required ... ok
test e2e_tool_error_contract_is_machine_readable ... ok
test e2e_output_get_name_resolution_metadata_and_ambiguity_candidates ... ok
test e2e_concurrent_create_same_name_rejects_one_process ... ok
test e2e_input_delete_pack_is_deterministic ... ok
test e2e_freshness_metadata_filters_and_warnings ... ok
test e2e_output_read_rejects_legacy_match_cursor_mode_fields ... ok
test e2e_finalize_validation_reports_missing_sections_and_invalid_refs ... ok
test e2e_request_id_and_revision_conflict_contract ... ok
test e2e_output_read_supports_profiles_contains_and_page_token ... ok
test e2e_tool_call_roundtrip_with_real_stdio ... ok
test e2e_multi_agent_handoff_compact_full_and_stale_path ... ok
test e2e_output_read_orchestrator_default_is_bounded_and_reviewer_is_full ... ok
test e2e_shutdown_notification_has_no_side_effects ... ok
test e2e_shutdown_exit_terminates_server ... ok

test result: ok. 25 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.23s

running 31 tests
test test_malformed_pack_file_is_recovered_by_list ... ok
test test_schema_mismatch_returns_migration_required ... ok
test test_list_with_query ... ok
test test_create_applies_tags ... ok
test test_name_resolution_ambiguity_exposes_candidate_ids ... ok
test test_finalize_empty_pack_rejected ... ok
test test_name_resolution_is_deterministic_and_prefers_finalized ... ok
test test_duplicate_name_is_rejected ... ok
test test_get_rendered_exposes_freshness_state_and_warning_when_expiring_soon ... ok
test test_finalize_pack_with_only_empty_section_rejected ... ok
test test_checked_mutation_rejects_stale_revision ... ok
test test_json_round_trip ... ok
test test_draft_workflow_remains_flexible_before_finalize ... ok
test test_touch_ttl_updates_revision_and_legend ... ok
test test_revision_increments ... ok
test test_upsert_section_update_preserves_order_without_explicit_order ... ok
test test_output_read_reviewer_profile_preserves_full_evidence ... ok
test test_full_pack_lifecycle ... ok
test test_finalize_rejects_ref_when_line_end_exceeds_file_length ... ok
test test_output_read_contains_filter ... ok
test test_revision_conflict_changed_section_keys_are_bounded ... ok
test test_output_read_page_token_paging_is_deterministic_and_validated ... ok
test test_output_read_executor_profile_is_actionable_compact ... ok
test test_delete_pack_action_recovers_corrupted_and_oversized_without_affecting_healthy_pack ... ok
test test_set_meta_empty_payload_rejected ... ok
test test_expired_pack_is_not_visible_immediately_in_list ... ok
test test_delete_section ... ok
test test_finalize_missing_qa_or_verdict_is_actionable ... ok
test test_list_pagination ... ok
test test_output_read_orchestrator_default_is_compact_and_bounded ... ok
test test_stale_ref_in_output ... ok

test result: ok. 31 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s

running 13 tests
test test_get_rendered_empty_identifier ... ok
test test_list_filtered_returns_packs ... ok
test test_resolve_by_name ... ok
test test_get_rendered_not_found_id ... ok
test test_get_rendered_status_filter_mismatch ... ok
test test_render_stale_ref_shown_as_warning ... ok
test test_render_with_name_and_brief ... ok
test test_render_legend_contains_id_and_status ... ok
test test_render_with_diagram_block ... ok
test test_lang_detection_rust_extension ... ok
test test_render_with_tags ... ok
test test_lang_detection_unknown_extension ... ok
test test_render_with_section_and_ref ... ok

test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s).\n\nContext pack:

[AmirTlinov]

VERDICT: PASS

PASS with no blocking findings.

• Document-only input.write snapshot contract and validate_only dry-run are implemented and tested.
• Legacy op/granular write usage is rejected with actionable guidance.
• Finalize fail-closed checks remain enforced for write paths.
• Scope remains limited to the requested files.

Verification artifacts: cargo test --all-targets --all-features (all tests passing on PR branch).

Context pack: pk_t4773pbv