Ziyu Dong b324c34f78 fix(ingest): never write a text capture through an existing entry ...

Binary captures pick their filename with lstat so they never replace an
existing directory entry (#4393). Text captures (webpages, tweets, arXiv)
still used Path.exists(), which follows symlinks: a dangling symlink named
like the capture reported "free" and write_text() followed it out of the
corpus directory. The loop also stopped at 999 numbered names and then
overwrote the last one. Share the lstat-based selection between both
paths.

(cherry picked from commit 3e483ca077)

2026-10-22 13:12:56 +01:00

..

fixtures

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__init__.py

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bench_extract.py

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bench_query_scoring.py

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conftest.py

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pi.test.ts

fix(pi): keep checking later glob targets after malformed hook output; document Pi 0.58.4+

2026-10-13 10:27:02 +01:00

test_affected_cli.py

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test_affected_defines.py

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test_affected_member_seed.py

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test_affected_overrides.py

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test_agents_platform.py

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test_alias_folding.py

fix(build): fold node confidence the same way as edges and hyperedges (#4529)

2026-10-20 10:35:23 +01:00

test_analyze.py

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test_anthropic_custom_endpoint.py

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test_antigravity_install.py

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test_apm_fallback_version.py

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test_architecture_doc.py

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test_astro_extraction.py

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test_astro_import_ids.py

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test_atomic_canvas_export.py

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test_atomic_version_stamp.py

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test_atomic_writes.py

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test_backend_env_isolation.py

feat(llm): opt-in backend selection, disable switch, and honest auto-detect (#4361)

2026-10-16 17:10:31 +01:00

test_backend_extras.py

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test_backend_opt_in.py

feat(llm): opt-in backend selection, disable switch, and honest auto-detect (#4361)

2026-10-16 17:10:31 +01:00

test_benchmark_raw_graph.py

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test_benchmark_real_query.py

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test_benchmark.py

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test_blade_extractor.py

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test_build_located_semantic_identity.py

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test_build_merge_dedup_scope.py

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test_build_merge_hyperedges_and_prune.py

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test_build_merge_shrink_guard.py

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test_build.py

fix(mcp): preserve parallel edges through graph.json round-trip and MCP output

2026-10-16 18:25:28 +01:00

test_builtin_global_type_refs.py

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test_c_include_resolution.py

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test_cache_stale_import_target.py

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test_cache.py

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test_callflow_html.py

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test_cargo_introspect.py

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test_cargo_missing_manifest.py

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test_carried_hyperedge_remap.py

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test_case_sensitive_resolution.py

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test_charmap_encoding.py

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test_chunking.py

fix(extract): keep edges between kept nodes when edge source_file is undispatched (#2276)

2026-10-13 22:21:43 +01:00

test_cjs_module_extension.py

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test_claude_cli_backend.py

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test_claude_md.py

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test_cli_broken_pipe.py

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test_cli_export.py

fix(mcp): preserve parallel edges through graph.json round-trip and MCP output

2026-10-16 18:25:28 +01:00

test_cli_help.py

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test_cloud_cta.py

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test_cluster_ambiguous_scale.py

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test_cluster_exclude_hubs.py

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test_cluster.py

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test_cobol_extractor.py

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test_code_only_update_all_hosts.py

test(skill): keep graphify off PATH and satisfy pyright in the update test

2026-10-16 17:14:07 +01:00

test_codebuddy.py

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test_community_hub_labels.py

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test_community_labels_skill.py

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test_compact_graph_json.py

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test_confidence.py

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test_corrupt_graph_json.py

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test_cpp_method_declarations.py

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test_cpp_nested_and_cli.py

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test_cpp_objc_cross_file_calls.py

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test_cpp_preprocess.py

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test_cpp_template_type_params.py

fix(extract): drop C++ template type parameters from references

2026-10-13 11:14:16 +01:00

test_cross_extension_reexport_self_cycle.py

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test_cross_language_call_resolution.py

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test_cross_repo_external_call_guards.py

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test_cross_repo_member_calls.py

Finish Objective-C member calls across a repository boundary (#3152)

2026-10-13 11:18:12 +01:00

test_cross_repo_shared_types.py

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test_csharp_call_site_generic_args.py

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test_csharp_delegate_declarations.py

fix(csharp): extract delegate declarations so references don't mint sourceless stubs

2026-10-20 10:35:24 +01:00

test_csharp_enum_members.py

fix(csharp): keep names that differ only by _ or case apart, in ids and in member-call keys (#4415)

2026-10-13 22:21:48 +01:00

test_csharp_field_generic_args.py

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test_csharp_foreach_loop_variable.py

feat(csharp): type foreach loop variables for receiver resolution

2026-10-13 22:21:48 +01:00

test_csharp_generic_callsites.py

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test_csharp_interface_dispatch.py

fix(dispatch): don't count gate-failing implementers toward confidence

2026-10-13 11:14:16 +01:00

test_csharp_member_calls.py

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test_csharp_member_chain_calls.py

fix(csharp): never bind a nameless member-call receiver to a same-named method in the file

2026-10-13 22:21:48 +01:00

test_csharp_member_nodes.py

fix(csharp): keep names that differ only by _ or case apart, in ids and in member-call keys (#4415)

2026-10-13 22:21:48 +01:00

test_csharp_object_creation.py

fix(csharp): new X() never binds to a method that shares X's name

2026-10-13 22:21:48 +01:00

test_csharp_partial_classes.py

fix(csharp): salt colliding ids before the partial merge, so a half keeps its members (#4411)

2026-10-13 22:21:43 +01:00

test_csharp_tuple_type_refs.py

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test_csharp_type_resolution.py

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test_csharp_underscore_collisions.py

fix(csharp): keep names that differ only by _ or case apart, in ids and in member-call keys (#4415)

2026-10-13 22:21:48 +01:00

test_csharp_var_call_return_type.py

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test_csharp_verbatim_interpolation.py

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test_dart.py

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test_dedup_remaps_hyperedges.py

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test_dedup_shrink_refuses_force_write.py

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test_dedup_survivor_richness.py

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test_dedup.py

Add a regression test for the source less collision survivor

2026-10-16 18:21:28 +01:00

test_definition_file_portability.py

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test_detect_jinja.py

fix(detect): classify Jinja templates as documents (#3427)

2026-10-13 22:21:43 +01:00

test_detect.py

fix(detect): classify extensionless scripts whose shebang names a versioned interpreter

2026-10-20 11:28:07 +01:00

test_devin.py

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test_docx_to_markdown.py

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test_dotnet.py

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test_duplicate_annotation_edges.py

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test_ejs_extractor.py

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test_elixir_defdelegate.py

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test_elixir_import_resolution.py

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test_elixir_keyword_def_calls.py

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test_elixir_qualified_calls.py

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test_elixir_unqualified_call_scope.py

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test_erlang_extractor.py

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test_evidence_binding.py

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test_explain_cli.py

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test_explain_same_file_tie.py

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test_export_control_characters.py

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test_export_direction.py

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test_export_idempotent_writes.py

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test_export_path_length.py

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test_export.py

fix(export): export GraphML from a graph loaded as a MultiGraph

2026-10-20 10:50:37 +01:00

test_ext_tagged_id_clash.py

fix(extract): keep a symbol that spells a sibling's old file id on its own node (#4449)

2026-10-14 22:53:26 +01:00

test_external_stub_endpoints.py

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test_extract_cache_location.py

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test_extract_cli.py

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test_extract_code_only_cli.py

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test_extract_path_memo.py

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test_extract_php_closures.py

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test_extract.py

fix(detect): classify extensionless scripts whose shebang names a versioned interpreter

2026-10-20 11:28:07 +01:00

test_extraction_spec_ids.py

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test_extractor_scan_root_context.py

fix(extractors): share the in-flight scan root via base, not graphify.extract (#3666)

2026-10-16 18:21:28 +01:00

test_extractors_registry.py

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test_falkordb_integration.py

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test_file_label_disambiguation.py

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test_file_node_id_spec.py

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test_file_slice.py

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test_file_truncation_warning.py

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test_forwarding_review_findings.py

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test_gemini_hook.py

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test_git_head_stdin.py

fix(mcp): don't hand git the server's stdin in _git_head (#4440)

2026-10-14 22:31:57 +01:00

test_global_add_tag_inference.py

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test_global_graph.py

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test_go_builtin_call_targets.py

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test_go_generic_receiver_methods.py

fix(go): normalize a generic receiver type before building its id

2026-10-13 22:53:44 +01:00

test_go_generic_type_params.py

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test_go_import_repoint.py

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test_go_interface_methods.py

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test_go_package_type_fold.py

fix(go): fold a package's type into one node when its methods span files (#3399)

2026-10-13 11:14:22 +01:00

test_go_qualified_resolution.py

test: pin in-file calls to salted Rust functions and Go ids outside a collision group

2026-10-16 17:12:53 +01:00

test_go_receiver_member_calls.py

test(go): pin both directions of per-function receiver scoping

2026-10-13 11:14:26 +01:00

test_god_nodes_cli.py

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test_god_nodes_exclude_hubs.py

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test_google_workspace.py

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test_grammar_cache_key.py

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test_graph_invariance.py

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test_graphdb_push_indexes.py

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test_hollow_chunks_arm_shrink_guard.py

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test_home_sandbox.py

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test_hook_chain_survives_skip.py

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test_hook_guard_token_match.py

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test_hook_guard.py

fix(hook): leave piped greps out of the nudge hint

2026-10-13 10:26:57 +01:00

test_hook_out_of_project_paths.py

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test_hook_strict.py

feat(hook): show the graph nodes behind a nudged call, and tighten its wording

2026-10-13 10:26:57 +01:00

test_hooks_rewrite.py

fix(hooks): rebuild after cherry-pick, rebase and pull --rebase (#4490)

2026-10-16 17:10:31 +01:00

test_hooks.py

fix(hooks): rebuild after cherry-pick, rebase and pull --rebase (#4490)

2026-10-16 17:10:31 +01:00

test_html_script_breakout.py

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test_html_theme.py

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test_hyperedge_member_shapes.py

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test_hyperedge_roundtrip.py

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test_hypergraph.py

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test_id_normalization_contract.py

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test_ignore_file_encoding.py

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test_image_vision.py

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test_import_extension_resolution.py

fix(resolution): resolve js imports to tsx sources

2026-10-13 11:14:16 +01:00

test_import_self_loops.py

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test_imported_export_forwarding.py

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test_incomplete_build_guard.py

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test_incremental_mtime_collision.py

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test_incremental_unscanned_placeholders.py

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test_incremental.py

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test_indirect_call_arrow_single_param_shadow.py

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test_indirect_call_block_scoped_shadow.py

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test_indirect_call_catch_binding_shadow.py

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test_indirect_call_external_import_shadow.py

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test_indirect_call_file_scope_callback_shadow.py

fix(js): shadow a file-scope callback's own params (#4448)

2026-10-14 22:31:57 +01:00

test_indirect_call_for_of_binding_shadow.py

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test_indirect_call_function_expression_shadow.py

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test_indirect_call_nested_closure_shadow.py

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test_indirect_dispatch_assign_return.py

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test_indirect_dispatch_getattr.py

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test_indirect_dispatch.py

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test_inferred_confidence_rubric.py

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test_ingest_url_type.py

fix(ingest): never write a text capture through an existing entry

2026-10-22 13:12:56 +01:00

test_ingest.py

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test_inherited_field_receivers.py

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test_injection_sentinel_coverage.py

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test_install_hook_identity.py

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test_install_line_endings.py

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test_install_references.py

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test_install_roundtrip.py

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test_install_strings.py

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test_install_upgrade.py

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test_install_version_stamp.py

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test_install_version_warning.py

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test_install.py

fix(codex): quote a spaced exe path in the PreToolUse hook command

2026-10-22 13:12:56 +01:00

test_issue_3405_python_resolution.py

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test_issue_3472_source_file_collision.py

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test_java_anonymous_class.py

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test_java_enum_members.py

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test_java_member_calls.py

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test_java_type_resolution.py

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test_js_callback_calls.py

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test_js_destructured_export.py

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test_js_dynamic_import_affected.py

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test_js_dynamic_imports.py

fix(js): anchor rescued external imports to the package, not the path leaf (#3084)

2026-10-12 23:02:50 +01:00

test_js_exported_fn_call_resolution.py

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test_js_exported_scalar_bindings.py

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test_js_import_resolution.py

fix(js): drop the barrel-named import edge once the import resolves past it (#4486)

2026-10-16 17:10:31 +01:00

test_js_member_call_bare_name_fallback.py

Add regression tests for the member call defer fix

2026-10-21 19:33:01 +01:00

test_js_member_collisions.py

fix(ts): don't guess between members the normalized key can't tell apart

2026-10-16 17:11:41 +01:00

test_js_module_level_anonymous_calls.py

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test_js_require_binding_shadow.py

fix(extract): a require binding does not shadow the required class

2026-10-21 19:33:10 +01:00

test_js_this_member_expressions.py

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test_js_walk_order.py

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test_jsconfig_baseurl.py

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test_json_schema_config.py

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test_jsx_component_usage_calls.py

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test_kotlin_generic_type_params.py

fix(extract): drop Kotlin generic type parameters from references

2026-10-13 11:14:16 +01:00

test_kotlin_grammar.py

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test_kotlin_object_literal.py

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test_kotlin_typealias_declarations.py

fix(kotlin): extract typealias declarations so references don't mint sourceless stubs

2026-10-20 10:35:23 +01:00

test_label_retry.py

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test_labeling.py

fix(llm): decode JSON escapes in community labels salvaged from a truncated reply

2026-10-20 10:35:22 +01:00

test_language_override_imports.py

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test_language_override_lifecycle.py

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test_language_overrides.py

fix(rcfile): read .graphifyrc with utf-8-sig so a BOM doesn't drop the first key

2026-10-20 10:35:22 +01:00

test_language_resolvers.py

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test_languages.py

fix(markdown): resolve wikilinks that start with the scan root's own folders (#4559)

2026-10-20 11:28:04 +01:00

test_llm_backends.py

fix(llm): pin source_file to the dispatched file in the extraction prompt

2026-10-16 17:10:31 +01:00

test_llm_null_token_counts.py

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test_llm_parser_reasoning.py

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test_llm_parser.py

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test_long_path_hashing.py

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test_lookup_exit_codes.py

fix(query): only refuse an EXACT-name ambiguity, not a search keyword (#4517)

2026-10-20 14:57:06 +01:00

test_loose_sibling_import_resolution.py

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test_lost_saved_semantic_nodes.py

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test_lua_import.py

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test_lua_method_calls.py

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test_manifest_ingest.py

fix(manifest_ingest): read only a POM's own dependencies

2026-10-21 19:33:01 +01:00

test_manifest_tomli_required.py

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test_markdown_code_spans.py

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test_mcp_graph_view_cache.py

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test_mcp_ingest.py

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test_merge_chunks_validation.py

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test_merge_graphs_cli.py

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test_merge_sweeps_reextract_orphans.py

fix(build): spare hyperedge members and pre-prune semantic isolates in orphan sweep (#4399)

2026-10-13 22:53:44 +01:00

test_minhash.py

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test_multigraph_compat.py

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test_multigraph_diagnostics.py

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test_multilang.py

fix(rust): resolve a forward reference to a type that keeps its id beside a case-only sibling

2026-10-16 17:12:53 +01:00

test_no_cluster_run_only_keys.py

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test_no_cluster_undeclared_endpoints.py

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test_no_dedup_flag.py

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test_node_id_canonical.py

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test_non_regular_files.py

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test_non_string_node_ids.py

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test_objc_callable_markers.py

Mark ObjC declarations with _callable / _callable_class (#3228)

2026-10-13 11:16:15 +01:00

test_objc_category_interfaces.py

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test_objc_enum_declarations.py

fix: preserve attributed Objective-C enum members

2026-10-13 11:14:16 +01:00

test_objc_field_table_remap.py

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test_objc_member_calls.py

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test_objc_property_ivar_receivers.py

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test_obsidian_dangling_member.py

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test_obsidian_filename_cap.py

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test_obsidian_unicode_tags.py

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test_obsidian_vault_migration.py

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test_ocaml.py

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test_office_incremental.py

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test_office_limits.py

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test_ollama_native_chat.py

send ollama requests to /api/chat so num_ctx actually applies

2026-10-14 22:53:26 +01:00

test_ollama_retry_cap.py

send ollama requests to /api/chat so num_ctx actually applies

2026-10-14 22:53:26 +01:00

test_ollama.py

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test_openai_custom_endpoint.py

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test_opencode_plugin_refresh.py

fix(cli): leave installed skills alone on version and help (#4545)

2026-10-20 11:28:03 +01:00

test_out_dir_evidence.py

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test_oversized_document_slicing.py

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test_owned_type_sources.py

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test_package_json_subpath_imports.py

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test_partial_cache.py

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test_partial_extraction_warning.py

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test_pascal_call_scoping.py

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test_pascal_resolution.py

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test_pascal.py

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test_path_cli.py

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test_paths.py

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test_pdf_extra_warning.py

fix(detect): warn when a PDF cannot be read instead of returning "" silently (#4527)

2026-10-20 11:28:05 +01:00

test_pdf_slicing.py

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test_pdf_token_estimate.py

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test_pg_introspect.py

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test_phantom_cross_package_call.py

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test_phantom_external_import.py

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test_php_language_construct_calls.py

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test_php_object_creation.py

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test_php_receiver_member_calls.py

feat(php): resolve instance member calls through the receiver's declared type

2026-10-13 11:14:30 +01:00

test_php_static_call_resolution.py

feat(php): resolve instance member calls through the receiver's declared type

2026-10-13 11:14:30 +01:00

test_php_type_resolution.py

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test_php_unparsed_casts.py

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test_pi_guard_install.py

feat(pi): add a native Pi guard extension that also loads in Oh My Pi

2026-10-13 10:27:02 +01:00

test_pin_hash_seed.py

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test_pipeline.py

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test_pr10_csharp_overrides.py

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test_pr10_resolution_overrides.py

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test_pr10_watch_overrides.py

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test_provider_registry.py

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test_prs.py

fix(prs): read StatusContext state when classifying CI

2026-10-20 10:50:36 +01:00

test_prune_sweeps_orphans.py

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test_python_decorators.py

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test_python_forward_ref_file_id.py

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test_python_import_never_resolves_to_itself.py

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test_python_import_resolution.py

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test_python_inherited_method_calls.py

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test_python_module_call_exact_name.py

test(python): module-call exact-name tests, incl. a cross-module negative

2026-10-20 10:55:51 +01:00

test_python_nested_class_identity.py

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test_python_parse_memoization.py

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test_python_property_reads.py

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test_python_pytest_fixture_receivers.py

test(python): pin that forwarded import edges only gate fixture calls on a rebuild

2026-10-16 17:11:42 +01:00

test_python_reexport_type_binding.py

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test_python_self_type_ref.py

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test_python_typed_receiver_calls.py

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test_python_underscore_resolution.py

fix(python): salt module-level class ids that collide with a function or class (#2810)

2026-10-16 17:11:41 +01:00

test_qualified_annotation_stub_bind.py

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test_query_cli.py

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test_query_fallback_edges.py

fix(query): retain visited-node relationships in fallback traversal

2026-10-13 22:53:44 +01:00

test_query_induced_edges.py

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test_query_mcp_direction.py

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test_query_names_its_graph.py

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test_query_seed_order.py

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test_query_seeds.py

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test_querylog.py

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test_r_extractor.py

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test_rationale.py

fix(extract): redact credential-shaped text from rationale labels

2026-10-20 10:53:04 +01:00

test_read_hook.py

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test_reflect.py

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test_relation_collapse_precedence.py

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test_replace_or_append_section.py

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test_report_gap_thresholds.py

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test_report.py

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test_resolve_memoization.py

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test_ruby_bare_self_send_calls.py

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test_ruby_resolution.py

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test_rust_anonymous_const.py

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test_rust_builtin_type_hubs.py

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test_rust_case_collisions.py

test: pin in-file calls to salted Rust functions and Go ids outside a collision group

2026-10-16 17:12:53 +01:00

test_rust_in_file_call_binding.py

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test_rust_macro_rules.py

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test_rust_self_member_calls.py

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test_rust_use_trees.py

test: a Rust use rooted at a child mod reaches its declaration (#4564)

2026-10-20 10:35:37 +01:00

test_scala_abstract_methods.py

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test_scala_context_bounds.py

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test_scala_generic_type_params.py

fix(extract): drop Scala generic type parameters from references

2026-10-13 11:14:16 +01:00

test_scala_given_instances.py

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test_scala_self_type.py

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test_scala_top_level_binding.py

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test_scala_type_definition.py

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test_scip_ingest.py

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test_search_hook.py

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test_security.py

test(security): reject URLs with embedded credentials

2026-10-21 19:32:46 +01:00

test_semantic_cache_basename_recovery.py

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test_semantic_cache_out_root.py

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test_semantic_cleanup.py

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test_semantic_fragment_sanitize.py

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test_semantic_id_remap_root.py

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test_semantic_origin_stamp.py

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test_semantic_similarity.py

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test_serve_http.py

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test_serve.py

fix(mcp): preserve parallel edges through graph.json round-trip and MCP output

2026-10-16 18:25:28 +01:00

test_settings_merge.py

…

test_skill_auto_refresh.py

fix(cli): leave installed skills alone on version and help (#4545)

2026-10-20 11:28:03 +01:00

test_skill_code_only_incremental_update.py

fix: materialize extraction for code-only incremental updates

2026-10-16 17:13:49 +01:00

test_skill_codex_semantic_merge.py

test: account for #3987 Step B3.5 block in the B3-merge skill tests

2026-10-20 16:56:09 +01:00

test_skill_no_backtick_substitution.py

test(skill): no command runs from backticks in -c "..." blocks

2026-10-16 17:13:54 +01:00

test_skill_part_a_explicit_root.py

…

test_skill_persisted_scan_options.py

…

test_skill_semantic_all_cached.py

test: account for #3987 Step B3.5 block in the B3-merge skill tests

2026-10-20 16:56:09 +01:00

test_skill_version_warning.py

…

test_skillgen_input_path_injection.py

…

test_skillgen.py

fix(skill): a partly-read file is no longer a silent, permanent loss

2026-10-20 15:40:39 +01:00

test_solidity_extractor.py

…

test_solidity_inherited_calls.py

feat(solidity): resolve calls, super calls and modifiers inherited from base contracts

2026-10-16 17:12:42 +01:00

test_source_file_encoding.py

…

test_source_key_memoization.py

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test_sourceless_call_targets.py

…

test_src_layout_import_resolution.py

…

test_stale_prune.py

…

test_stat_index_husk.py

…

test_stat_index_multi_root.py

…

test_stat_index_portability.py

…

test_suggest_questions_ambiguous.py

…

test_svelte_extraction.py

…

test_swift_builtin_noise.py

…

test_swift_computed_properties.py

…

test_swift_cross_file_calls.py

…

test_swift_generic_type_params.py

fix(extract): drop Swift generic type parameters from references

2026-10-13 11:14:16 +01:00

test_swift_import_resolution.py

…

test_swift_macro_declarations.py

fix(swift): extract macro declarations and resolve freestanding macro calls

2026-10-20 10:35:25 +01:00

test_swift_protocol_dispatch.py

feat(dispatch): link interface members to every implementer, not just one

2026-10-13 11:14:16 +01:00

test_swift_protocol_requirements.py

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test_swift_self_type_ref.py

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test_symbol_resolution.py

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test_terraform_modules.py

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test_terraform.py

…

test_trailing_newline_not_a_syntax_error.py

…

test_transcribe.py

…

test_tree_html.py

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test_truncation_full_answer.py

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test_ts_abstract_methods.py

…

test_ts_decorators.py

…

test_ts_export_type_star.py

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test_ts_generators.py

…

test_ts_import_require.py

…

test_ts_import_type_arguments.py

…

test_ts_inheritance.py

…

test_ts_namespace.py

…

test_ts_new_expression_calls.py

…

test_ts_parse_warning.py

…

test_ts_receiver_member_calls.py

test(ts): cover method-assigned field receivers

2026-10-16 17:11:41 +01:00

test_type_only_import_cycles.py

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test_typescript_enum_members.py

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test_typescript_module_extensions.py

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test_uninstall_purge_safety.py

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test_uninstall_scope.py

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test_uninstall_symlink.py

…

test_unmapped_at_alias_resolution.py

fix(js): keep import edges to declared npm packages (#3084)

2026-10-12 23:02:50 +01:00

test_unverified_semantic_shrink.py

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test_validate.py

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test_vbnet_extractor.py

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test_vue_extraction.py

…

test_walk_python_tree_iterative.py

…

test_watch_identity_cache.py

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test_watch_manifest_location.py

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test_watch.py

fix(cluster): keep a community label when membership overlap stays a majority (#2298)

2026-10-14 22:53:26 +01:00

test_wheel_packaging.py

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test_wiki_link_filename_parity.py

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test_wiki_truncation_indicator.py

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test_wiki.py

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test_word_count_cache.py

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test_zero_node_no_cache.py

…