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skills/bioskills/bio-clip-seq-crosslink-site-detection/SKILL.md
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skills/bioskills/bio-clip-seq-differential-clip/SKILL.md
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skills/bioskills/bio-crispr-screens-screen-qc/SKILL.md
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skills/bioskills/bio-data-visualization-circos-plots/SKILL.md
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skills/bioskills/bio-data-visualization-color-palettes/scripts/palettes_phd.R
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skills/bioskills/bio-data-visualization-ggplot2-fundamentals/SKILL.md
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skills/bioskills/bio-data-visualization-network-visualization/scripts/interactive_network.py
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skills/bioskills/bio-data-visualization-volcano-and-ma-plots/SKILL.md
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skills/bioskills/bio-database-access-batch-downloads/scripts/batch_fasta.py
skills/bioskills/bio-database-access-batch-downloads/scripts/robust_download.py
skills/bioskills/bio-database-access-biomart-queries/SKILL.md
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skills/bioskills/bio-database-access-biomart-queries/scripts/bulk_id_mapping.py
skills/bioskills/bio-database-access-biomart-queries/scripts/coordinate_table.sh
skills/bioskills/bio-database-access-biomart-queries/scripts/ortholog_table.py
skills/bioskills/bio-database-access-blast-searches/SKILL.md
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skills/bioskills/bio-database-access-blast-searches/scripts/blastp_filtered.py
skills/bioskills/bio-database-access-blast-searches/scripts/save_and_parse.py
skills/bioskills/bio-database-access-ensembl-rest/SKILL.md
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skills/bioskills/bio-database-access-ensembl-rest/scripts/lookup_and_overlap.py
skills/bioskills/bio-database-access-ensembl-rest/scripts/vep_annotation.py
skills/bioskills/bio-database-access-entrez-fetch/SKILL.md
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skills/bioskills/bio-database-access-entrez-fetch/scripts/fetch_pubmed.py
skills/bioskills/bio-database-access-entrez-fetch/scripts/fetch_sequences.py
skills/bioskills/bio-database-access-entrez-fetch/scripts/fetch_summaries.py
skills/bioskills/bio-database-access-entrez-link/SKILL.md
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skills/bioskills/bio-database-access-entrez-link/scripts/chain_links.py
skills/bioskills/bio-database-access-entrez-link/scripts/discover_links.py
skills/bioskills/bio-database-access-entrez-search/SKILL.md
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skills/bioskills/bio-database-access-entrez-search/scripts/database_info.py
skills/bioskills/bio-database-access-entrez-search/scripts/global_query.py
skills/bioskills/bio-database-access-geo-data/SKILL.md
skills/bioskills/bio-database-access-geo-data/references/usage-guide.md
skills/bioskills/bio-database-access-geo-data/scripts/geo_from_pubmed.py
skills/bioskills/bio-database-access-geo-data/scripts/geo_to_sra.py
skills/bioskills/bio-database-access-geo-data/scripts/search_geo.py
skills/bioskills/bio-database-access-interaction-databases/SKILL.md
skills/bioskills/bio-database-access-interaction-databases/references/usage-guide.md
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skills/bioskills/bio-database-access-interaction-databases/scripts/string_network.py
skills/bioskills/bio-database-access-local-blast/SKILL.md
skills/bioskills/bio-database-access-local-blast/references/usage-guide.md
skills/bioskills/bio-database-access-local-blast/scripts/blast_wrapper.py
skills/bioskills/bio-database-access-local-blast/scripts/create_database.sh
skills/bioskills/bio-database-access-local-blast/scripts/reciprocal_best.sh
skills/bioskills/bio-database-access-local-blast/scripts/run_blast.sh
skills/bioskills/bio-database-access-ncbi-datasets-cli/SKILL.md
skills/bioskills/bio-database-access-ncbi-datasets-cli/references/usage-guide.md
skills/bioskills/bio-database-access-ncbi-datasets-cli/scripts/bulk_dehydrated.sh
skills/bioskills/bio-database-access-ncbi-datasets-cli/scripts/download_genome.sh
skills/bioskills/bio-database-access-ncbi-datasets-cli/scripts/gene_metadata.sh
skills/bioskills/bio-database-access-ortholog-inference/SKILL.md
skills/bioskills/bio-database-access-ortholog-inference/references/usage-guide.md
skills/bioskills/bio-database-access-ortholog-inference/scripts/compara_orthologs.py
skills/bioskills/bio-database-access-ortholog-inference/scripts/cross_resource.py
skills/bioskills/bio-database-access-ortholog-inference/scripts/kegg_orthology.py
skills/bioskills/bio-database-access-remote-homology/SKILL.md
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skills/bioskills/bio-database-access-remote-homology/scripts/foldseek_search.sh
skills/bioskills/bio-database-access-remote-homology/scripts/iterative_profile.sh
skills/bioskills/bio-database-access-remote-homology/scripts/pfam_annotation.sh
skills/bioskills/bio-database-access-sra-data/SKILL.md
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skills/bioskills/bio-database-access-sra-data/scripts/download_single.sh
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skills/bioskills/bio-database-access-uniprot-access/SKILL.md
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skills/bioskills/bio-database-access-uniprot-access/scripts/uniprot_query.py
skills/bioskills/bio-differential-expression-batch-correction/SKILL.md
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skills/bioskills/bio-differential-expression-de-results/SKILL.md
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skills/bioskills/bio-differential-expression-de-results/scripts/export_excel.R
skills/bioskills/bio-differential-expression-de-results/scripts/filter_results.R
skills/bioskills/bio-differential-expression-de-visualization/SKILL.md
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skills/bioskills/bio-differential-expression-de-visualization/scripts/pca_plot.R
skills/bioskills/bio-differential-expression-de-visualization/scripts/volcano_plot.R
skills/bioskills/bio-differential-expression-deseq2-basics/SKILL.md
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skills/bioskills/bio-differential-expression-deseq2-basics/scripts/multi_condition.R
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skills/bioskills/bio-differential-expression-edger-basics/scripts/contrasts.R
skills/bioskills/bio-differential-expression-timeseries-de/SKILL.md
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skills/bioskills/bio-ecological-genomics-biodiversity-metrics/SKILL.md
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skills/bioskills/bio-ecological-genomics-species-delimitation/SKILL.md
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skills/bioskills/bio-epidemiological-genomics-amr-surveillance/SKILL.md
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skills/bioskills/bio-epidemiological-genomics-pathogen-typing/SKILL.md
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skills/bioskills/bio-epidemiological-genomics-phylodynamics/SKILL.md
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skills/bioskills/bio-epidemiological-genomics-transmission-inference/SKILL.md
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skills/bioskills/bio-epidemiological-genomics-variant-surveillance/SKILL.md
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skills/bioskills/bio-epitranscriptomics-m6a-differential/SKILL.md
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skills/bioskills/bio-epitranscriptomics-modification-visualization/SKILL.md
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skills/bioskills/bio-epitranscriptomics-modification-visualization/scripts/deeptools_metagene.sh
skills/bioskills/bio-epitranscriptomics-modification-visualization/scripts/guitar_metagene.R
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skills/bioskills/bio-experimental-design-multiple-testing/SKILL.md
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skills/bioskills/bio-experimental-design-randomization-blocking/SKILL.md
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skills/bioskills/bio-experimental-design-sample-size/SKILL.md
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skills/bioskills/bio-expression-matrix-counts-ingest/SKILL.md
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skills/bioskills/bio-expression-matrix-counts-ingest/scripts/load_counts.py
skills/bioskills/bio-expression-matrix-gene-id-mapping/SKILL.md
skills/bioskills/bio-expression-matrix-gene-id-mapping/references/usage-guide.md
skills/bioskills/bio-expression-matrix-gene-id-mapping/scripts/map_gene_ids.py
skills/bioskills/bio-expression-matrix-metadata-joins/SKILL.md
skills/bioskills/bio-expression-matrix-metadata-joins/references/usage-guide.md
skills/bioskills/bio-expression-matrix-metadata-joins/scripts/join_metadata.py
skills/bioskills/bio-expression-matrix-normalization/SKILL.md
skills/bioskills/bio-expression-matrix-normalization/references/usage-guide.md
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skills/bioskills/bio-expression-matrix-sparse-handling/SKILL.md
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tests/test_byoc_confinement_scope.py
tests/test_capability_state.py
tests/test_catalyst_sar_screening.py
tests/test_cell_cancelled_during_bootstrap.py
tests/test_cell_dependencies.py
tests/test_cell_execution_service.py
tests/test_cell_watchdog.py
tests/test_channel_counter_contract.py
tests/test_check_css_tokens.py
tests/test_checkpoint_binding_survival.py
tests/test_checkpoint_state_snapshots.py
tests/test_ci_gate_independence.py
tests/test_citation_metadata.py
tests/test_cli_auto_mode.py
tests/test_cli_catalog_posture.py
tests/test_cli_code_mode_test_runner.py
tests/test_cli_contract.py
tests/test_cli_daemon_api_root.py
tests/test_cli_stop_slow_daemon.py
tests/test_cluster_session_e2e.py
tests/test_cluster_session_production_wiring.py
tests/test_code_evidence.py
tests/test_compaction_chunked_summary.py
tests/test_compaction_cli_budget.py
tests/test_compaction_externalize_retrieval.py
tests/test_compaction_failure_breaker.py
tests/test_compaction_ledger.py
tests/test_compaction_summary_robustness.py
tests/test_compaction_wave2_integration.py
tests/test_compaction_wave3_integration.py
tests/test_compaction_wave4_review.py
tests/test_completion_delivery.py
tests/test_completion_gate.py
tests/test_compute_alias_registration.py
tests/test_compute_durability.py
tests/test_compute_harvest_safety.py
tests/test_compute_job_races.py
tests/test_compute_lifecycle.py
tests/test_compute_manifest.py
tests/test_compute_nvidia.py
tests/test_compute_output_caps.py
tests/test_compute_owner_and_harvest.py
tests/test_compute_session_routes.py
tests/test_compute_states.py
tests/test_compute_task_centre.py
tests/test_compute_trust_boundary.py
tests/test_config.py
tests/test_connector_canary.py
tests/test_connector_manifests.py
tests/test_connector_repository.py
tests/test_container_deployment.py
tests/test_context_policy_web.py
tests/test_contract_inventory.py
tests/test_dangerous_tool_declaration.py
tests/test_data_background_tools.py
tests/test_data_dir_permissions.py
tests/test_datapro_index.py
tests/test_delegated_cell_record.py
tests/test_delegation_control.py
tests/test_delegation_env_inheritance.py
tests/test_delegation_idempotency.py
tests/test_delegation_null_semantics.py
tests/test_delegation_persistence.py
tests/test_delegation_policy.py
tests/test_delegation_runtime.py
tests/test_delegation_step_projection.py
tests/test_delegation_task_status.py
tests/test_delegation_workspace.py
tests/test_diagnostic_archive_boundary.py
tests/test_diagnostics.py
tests/test_diagnostics_routes.py
tests/test_doctor.py
tests/test_doubao_search.py
tests/test_dynamic_tool_scopes.py
tests/test_dynamic_tools.py
tests/test_e2e.py
tests/test_egress.py
tests/test_egress_surface.py
tests/test_endpoint_probe_guard.py
tests/test_env_generations.py
tests/test_env_kernel_binding.py
tests/test_env_provenance_confidence.py
tests/test_env_setup_failure_projection.py
tests/test_environment_readiness.py
tests/test_environments.py
tests/test_error_envelope.py
tests/test_evidence_adapters.py
tests/test_evidence_snapshot.py
tests/test_evidence_verification.py
tests/test_evidence_walkthrough_provenance.py
tests/test_execution_coordinator.py
tests/test_execution_principal.py
tests/test_execution_sources.py
tests/test_execution_view_service.py
tests/test_first_run_access.py
tests/test_first_run_without_secret_store.py
tests/test_followup_admission.py
tests/test_frame_cap_units.py
tests/test_frame_pagination.py
tests/test_frame_repository.py
tests/test_fsprobe.py
tests/test_gateway.py
tests/test_gateway_engine.py
tests/test_gateway_host_allowlist.py
tests/test_gateway_kernel_lifecycle.py
tests/test_gateway_kernel_routes.py
tests/test_gateway_lazy_runtime.py
tests/test_gateway_session_domain_routes.py
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tests/test_gateway_static_cache.py
tests/test_gateway_webui_next.py
tests/test_global_research_views.py
tests/test_governance.py
tests/test_guardian_enforce.py
tests/test_guardian_shadow.py
tests/test_harness_characterization.py
tests/test_harness_contract.py
tests/test_harvest_remote_provenance.py
tests/test_host_accelerators.py
tests/test_host_completion_service.py
tests/test_host_contract.py
tests/test_host_credentials_service.py
tests/test_host_data_service.py
tests/test_host_delegation_service.py
tests/test_host_endpoint_service.py
tests/test_host_llm_service.py
tests/test_host_mcp_service.py
tests/test_host_network_capability.py
tests/test_host_progress_service.py
tests/test_host_remote_capability_service.py
tests/test_host_remote_science_service.py
tests/test_host_skill_service.py
tests/test_host_workspace_service.py
tests/test_image_attachment_budget.py
tests/test_import_bioskills.py
tests/test_jupyter_adapter.py
tests/test_kernel.py
tests/test_kernel_font_cache.py
tests/test_kernel_generation_storage.py
tests/test_kernel_generation_supervisor.py
tests/test_kernel_oversized_frame.py
tests/test_kernel_recovery.py
tests/test_kernel_sandbox.py
tests/test_kernel_supervisor.py
tests/test_lazy_kernel.py
tests/test_llm_anthropic_streaming.py
tests/test_llm_anthropic_tool_calls.py
tests/test_llm_capabilities.py
tests/test_llm_gemini_tool_calls.py
tests/test_llm_openai_tool_calls.py
tests/test_llm_providers.py
tests/test_llm_responses_tool_calls.py
tests/test_llm_system_placement.py
tests/test_llm_transport_typed.py
tests/test_llm_transport_wiring.py
tests/test_local_job_envelope.py
tests/test_local_job_lifecycle.py
tests/test_local_jobs.py
tests/test_local_model_discovery.py
tests/test_marker_policy.py
tests/test_materialisation_atomicity.py
tests/test_mcp_client.py
tests/test_mcp_control_tools.py
tests/test_mcp_lifecycle.py
tests/test_mcp_tools_positional_server.py
tests/test_memory_budget.py
tests/test_memory_edit_and_expiry_quota.py
tests/test_memory_repository.py
tests/test_memory_scope_and_budgets.py
tests/test_message_pagination.py
tests/test_message_paging_client.py
tests/test_metadata_repositories.py
tests/test_methodology_skills.py
tests/test_mineral_spectra_analysis.py
tests/test_model_admission.py
tests/test_model_assets.py
tests/test_model_binding_recovery.py
tests/test_model_capability_receipts.py
tests/test_model_catalog.py
tests/test_model_profile_identity.py
tests/test_model_profile_probe_reachable.py
tests/test_model_profile_readiness.py
tests/test_model_protocol_menu.py
tests/test_model_revision_binding.py
tests/test_native_tools.py
tests/test_notebook_export.py
tests/test_notebook_lineage.py
tests/test_observability.py
tests/test_onboarding.py
tests/test_orchestration_backend_opacity.py
tests/test_orchestration_distributed.py
tests/test_orchestration_reconciler.py
tests/test_orchestration_routes.py
tests/test_orchestration_session.py
tests/test_orchestration_skills.py
tests/test_orchestration_slurm.py
tests/test_permission_repository.py
tests/test_permissions.py
tests/test_plan.py
tests/test_plan_crosswalk.py
tests/test_plan_repository.py
tests/test_plan_resume_claim.py
tests/test_plan_service.py
tests/test_platform_support.py
tests/test_ports_helper.py
tests/test_preinstall_probe_confinement.py
tests/test_preinstall_uv_fallback.py
tests/test_producer_output_budgets.py
tests/test_progress_document.py
tests/test_project_paging.py
tests/test_protein_design_mcp.py
tests/test_protein_mutation_enhancement_skill.py
tests/test_prov_record_confinement.py
tests/test_provenance_identity.py
tests/test_provenance_paths.py
tests/test_public_api_contract.py
tests/test_public_exception_projector.py
tests/test_query_authorizer_lifecycle.py
tests/test_query_scoping_team_mode.py
tests/test_queued_followups.py
tests/test_r_kernel.py
tests/test_recovery_recipe.py
tests/test_release_docs.py
tests/test_release_gate_manifest.py
tests/test_release_gates.py
tests/test_release_pipeline.py
tests/test_release_rehearsal.py
tests/test_remote_capability_probe.py
tests/test_remote_compute_control_tools.py
tests/test_renderer_capability_honesty.py
tests/test_renderer_registry.py
tests/test_resource_allowlist.py
tests/test_response_capture_assembly.py
tests/test_response_contract_coverage.py
tests/test_response_contract_downloads.py
tests/test_response_schemas.py
tests/test_retrieval_provenance.py
tests/test_retrieval_source.py
tests/test_retrosynthesis_evaluator.py
tests/test_retrosynthesis_evidence_regressions.py
tests/test_retrosynthesis_generated_programs.py
tests/test_retrosynthesis_generation.py
tests/test_retrosynthesis_planning.py
tests/test_retrosynthesis_scenario_protocols.py
tests/test_retrosynthesis_scoring_regressions.py
tests/test_revert_projection.py
tests/test_review.py
tests/test_review_finding_identity.py
tests/test_review_scratch.py
tests/test_review_service.py
tests/test_sandbox_credential_denies.py
tests/test_sandbox_grants.py
tests/test_schema_migrations.py
tests/test_science_connectors.py
tests/test_science_control_tools.py
tests/test_scientific_review_golden.py
tests/test_scientific_review_service.py
tests/test_scientific_reviewer.py
tests/test_sdk_compute.py
tests/test_secret_broker.py
tests/test_secret_canary.py
tests/test_security.py
tests/test_security_headers.py
tests/test_server_agent_run.py
tests/test_server_completions.py
tests/test_server_errors_module.py
tests/test_server_execution_coordinator.py
tests/test_session_and_message_paging.py
tests/test_session_branching.py
tests/test_session_control_tools.py
tests/test_session_deletion.py
tests/test_session_domain_service.py
tests/test_session_package.py
tests/test_session_recovery.py
tests/test_session_sidebar_scope.py
tests/test_session_snapshots.py
tests/test_session_title_service.py
tests/test_session_tool_catalog.py
tests/test_settings_repository.py
tests/test_setup_environments.py
tests/test_share_expiry.py
tests/test_share_gateway.py
tests/test_share_import.py
tests/test_share_projection.py
tests/test_share_protocol.py
tests/test_share_relay_tunnel.py
tests/test_share_router.py
tests/test_share_service.py
tests/test_share_viewer.py
tests/test_single_cell_rna_analysis_skill.py
tests/test_skill_catalog_readiness_route.py
tests/test_skill_customization_service.py
tests/test_skill_frontmatter_edit.py
tests/test_skill_network_contract.py
tests/test_skill_product_surface.py
tests/test_skill_recipes_are_callable.py
tests/test_skill_reference_reading.py
tests/test_skill_requirements.py
tests/test_skill_sidecar_recovery.py
tests/test_skill_versions.py
tests/test_skill_write_authorization.py
tests/test_skills.py
tests/test_skills_installer_contract.py
tests/test_specialist_allowlist_armed.py
tests/test_specialist_connector_allowlist.py
tests/test_specialist_delegation_roundtrip.py
tests/test_specialists_builtin.py
tests/test_stage10_connectors.py
tests/test_stage10_live_canaries.py
tests/test_stage11_remote_compute.py
tests/test_stage12_ga.py
tests/test_stage1_browser_fixture.py
tests/test_stage4_atomic_promotion.py
tests/test_stage4_candidate_promotion.py
tests/test_startup_no_implicit_install.py
tests/test_startup_no_implicit_side_effects.py
tests/test_stop_kernel_drains_queue.py
tests/test_store.py
tests/test_structured_finalize.py
tests/test_submit_output_reconciliation.py
tests/test_table_profile.py
tests/test_task_modes.py
tests/test_team_auth_routes.py
tests/test_team_cli.py
tests/test_team_files.py
tests/test_team_governance.py
tests/test_team_governance_routes.py
tests/test_team_isolation_hardening.py
tests/test_team_repository.py
tests/test_team_session_ownership.py
tests/test_team_ws_isolation.py
tests/test_telemetry_collector.py
tests/test_telemetry_consent.py
tests/test_telemetry_consent_route.py
tests/test_telemetry_emit.py
tests/test_telemetry_off_by_default.py
tests/test_telemetry_schema.py
tests/test_telemetry_transmission.py
tests/test_token_mint_atomicity.py
tests/test_token_query_bootstrap.py
tests/test_tool_schema.py
tests/test_tools.py
tests/test_unbounded_session_memory.py
tests/test_unstarted_worker_admission.py
tests/test_update_contributors.py
tests/test_upload_scope_resolution.py
tests/test_user_llm_keys.py
tests/test_variable_inspector_service.py
tests/test_volcengine_connector.py
tests/test_web_onboarding.py
tests/test_webtools.py
tests/test_webtools_redirect_guard.py
tests/test_webui_static_contract.py
tests/test_workbench_state_service.py
tests/test_worker_runtime_alias.py
tests/test_worker_tcp_transport.py
tests/test_workspace_scan_deadline.py
tests/test_workspace_streaming_budgets.py
tests/test_write_file_atomicity.py
tests/test_ws_frames.py
tests/test_ws_resume_cursor.py
tests/test_wsl_parity.py
workflows/README.md
workflows/README_zh.md
workflows/next-round-acceptance.json
workflows/artifact-lineage/README.md
workflows/artifact-lineage/README_zh.md
workflows/artifact-lineage/workflow.json
workflows/codebase-mode/README.md
workflows/codebase-mode/README_zh.md
workflows/codebase-mode/workflow.json
workflows/delegation/README.md
workflows/delegation/README_zh.md
workflows/delegation/workflow.json
workflows/environment-provenance/README.md
workflows/environment-provenance/README_zh.md
workflows/environment-provenance/workflow.json
workflows/environment-transaction/README.md
workflows/environment-transaction/README_zh.md
workflows/environment-transaction/workflow.json
workflows/evidence-package/README.md
workflows/evidence-package/README_zh.md
workflows/evidence-package/workflow.json
workflows/permission-boundary/README.md
workflows/permission-boundary/README_zh.md
workflows/permission-boundary/workflow.json
workflows/python-analysis/README.md
workflows/python-analysis/README_zh.md
workflows/python-analysis/workflow.json
workflows/r-analysis/README.md
workflows/r-analysis/README_zh.md
workflows/r-analysis/workflow.json
workflows/remote-compute/README.md
workflows/remote-compute/README_zh.md
workflows/remote-compute/workflow.json
workflows/science-retrieval/README.md
workflows/science-retrieval/README_zh.md
workflows/science-retrieval/workflow.json
workflows/telemetry-identity/README.md
workflows/telemetry-identity/README_zh.md
workflows/telemetry-identity/workflow.json
workflows/tool-bringup/README.md
workflows/tool-bringup/README_zh.md
workflows/tool-bringup/workflow.json