feat: confluence benchmark, pattern extractor, agent KB, UX spec

- extract-patterns.js: mines layered arch, ArgoCD appsets, cloud regions,
  CIDR allocations, naming conventions, sync waves, tech stack from code
- agent-kb.js: token-efficient JSON rendering of same doc tree
- eval-confluence-ref-questions.json: 32 reference-only benchmark questions
- wiggum-v2.sh: Ralph Wiggum loop targeting confluence baseline (77.8%)
- docs/human-ux-spec.md: BMad UX designer spec for human doc structure
- Eval results: V2 at 28.7% vs confluence 77.8% baseline
- Hub/spoke ownership now correctly extracted (95% on that question)
- Naming conventions, regions, CIDRs surfaced in system-architecture.md

foxtrot-docs-v3/reference/subsystems/runtime.md

@@ -0,0 +1,79 @@
+# Subsystem: runtime
+
+**Kind:** domain
+**Files:** 16309
+**Functions:** 69, **Classes:** 0
+
+## Structural Notes
+- 69 functions with no classes — procedural/script-heavy architecture
+- Isolated subsystem with no cross-subsystem dependencies — may be self-contained tooling or unused
+
+## Public Exports
+- `ci_scripts`
+- `format_error`
+- `load_generate_name_module`
+- `load_logging_utils`
+- `load_module`
+- `load_scan_inventory_module`
+- `load_schema`
+- `manifest_file`
+- `manifest_without_name`
+- `run_script`
+- `sample_inventory`
+- `test_ci_pipeline_validation_flow`
+- `test_clone_or_update_repo_https`
+- `test_clone_or_update_repo_missing_workspace`
+- `test_clone_or_update_repo_ssh`
+- `test_clone_or_update_repo_uses_existing`
+- `test_commit_files_to_branch`
+- `test_create_pull_request_returns_url`
+- `test_deduplicate_environments`
+- `test_directories_exist`
+- `test_dockerfile_basics`
+- `test_error_logging_includes_remediation`
+- `test_extract_environment_info_invalid`
+- `test_extract_environment_info_valid`
+- `test_extract_pr_id_from_url`
+- `test_extract_spec_missing_fields`
+- `test_find_lowest_unused_index_empty`
+- `test_find_lowest_unused_index_gap`
+- `test_find_lowest_unused_index_no_gap`
+- `test_generate_app_config_contains_expected_paths`
+- `test_generate_argo_params_contains_destination`
+- `test_generate_compute_config_contains_expected_paths`
+- `test_generate_name_main_updates_manifest`
+- `test_generate_network_config_contains_expected_paths`
+- `test_gitignore_patterns_present`
+- `test_invalid_cloud_has_clear_error`
+- `test_invalid_phase_has_clear_error`
+- `test_invalid_type_has_clear_error`
+- `test_invalid_yaml_exits_one_with_clear_message`
+- `test_log_format_is_structured`
+- `test_manifest_lifecycle_new_environment`
+- `test_manifest_lifecycle_with_existing_environments`
+- `test_missing_file_returns_error`
+- `test_missing_required_field_has_clear_error`
+- `test_missing_required_field_has_line_number`
+- `test_missing_spec_cloud_has_clear_error`
+- `test_orchestrate_full_provision`
+- `test_parse_log_line`
+- `test_provision_app_calls_bitbucket`
+- `test_provision_app_requires_compute_complete`
+- `test_provision_compute_calls_bitbucket`
+- `test_provision_compute_requires_network_complete`
+- `test_provision_network_calls_bitbucket`
+- `test_required_files_exist`
+- `test_requirements_include_dependencies`
+- `test_run_inventory_scan_uses_env_file`
+- `test_save_manifest_preserves_content`
+- `test_scan_repo_for_environments`
+- `test_taskfile_has_required_tasks`
+- `test_update_manifest_adds_metadata`
+- `test_update_manifest_annotations`
+- `test_valid_manifest_passes`
+- `test_valid_yaml_exits_zero`
+- `test_wait_for_pr_merge_declined`
+- `test_wait_for_pr_merge_success`
+- `test_wait_for_pr_merge_timeout`
+- `valid_manifest`
+- `validate_manifest`