Ryan Peterson 8cfebfdfd2 fix(markdown): honour dotted qualifiers and explicit relative cites in mention resolution ...

Three findings from the automated review of #3562, all reproduced:

A dotted span with a non-code extension (README.md, pyproject.toml) was classified as a
symbol because only CODE_EXTENSIONS was checked, and every dotted form was reduced to its
last segment, so time.sleep matched a repo's own sleep(). The dotted form now keeps its
whole chain, the file early-exit also checks DOC_EXTENSIONS, and a bare-name match must
carry every qualifier as an owner label or a segment or stem of its source path.

_match_cited_file used lstrip("./"), which strips characters, so a .github/... cite could
never match by suffix. The leading ./ and ../ segments are now stripped as segments, and
the suffix form also matches a root-level file.

An explicit ./ or ../ cite that escaped the corpus fell through to the suffix rule and
could land on an unrelated copy of the file. It now resolves relative to the document
only.

(cherry picked from commit 3f84e7f3e2)

2026-09-16 14:50:54 +01:00

..

fixtures

fix(rust): extract module-level static and const declarations

2026-09-10 22:44:38 +01:00

__init__.py

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bench_extract.py

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bench_query_scoring.py

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conftest.py

test: isolate backend-detection tests from the developer's environment

2026-09-10 23:04:40 +01:00

test_affected_cli.py

test(affected): cover outside-root clean-miss and non-out-dir graph layout (#2706)

2026-08-15 17:16:53 +01:00

test_affected_member_seed.py

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test_agents_platform.py

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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

fix(export): write graph.canvas and Obsidian notes atomically

2026-09-05 01:18:59 +01:00

test_atomic_version_stamp.py

fix(install): write .graphify_version atomically via os.replace

2026-09-05 01:18:59 +01:00

test_atomic_writes.py

Guard os_replace_with_fallback against src equal to dst

2026-09-12 17:36:09 +01:00

test_backend_env_isolation.py

test: isolate backend-detection tests from the developer's environment

2026-09-10 23:04:40 +01:00

test_backend_extras.py

release: 0.9.61 — fix Python 3.12/3.13 breakage from 0.9.60

2026-09-12 22:23:00 +01:00

test_benchmark_raw_graph.py

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test_benchmark.py

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test_build_merge_dedup_scope.py

Scope deduplication during incremental merges

2026-09-11 22:46:15 +01:00

test_build_merge_hyperedges_and_prune.py

fix: support Python 3.14 optional dependencies

2026-09-12 21:33:43 +01:00

test_build_merge_shrink_guard.py

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test_build.py

Import Iterable in build.py, the annotations already use it

2026-09-10 14:03:22 +01:00

test_builtin_global_type_refs.py

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test_cache.py

Use the replace fallback for AST cache writes

2026-09-12 17:36:09 +01:00

test_callflow_html.py

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test_cargo_introspect.py

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test_carried_hyperedge_remap.py

test: route carried-hyperedge dedup through a re-extracted chunk (#3503)

2026-09-11 22:51:35 +01:00

test_case_sensitive_resolution.py

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test_charmap_encoding.py

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test_chunking.py

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test_cjs_module_extension.py

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test_claude_cli_backend.py

fix(claude-cli): tolerate a diagnostic preamble before the JSON envelope

2026-09-05 21:55:34 +01:00

test_claude_md.py

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test_cli_broken_pipe.py

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test_cli_export.py

fix: prefer top-level hyperedges in export

2026-09-05 01:18:59 +01:00

test_cli_help.py

fix(cli): list prs, provider, and export formats in --help

2026-08-29 19:32:51 +01:00

test_cluster.py

test(cluster): add the self-loop cohesion_score regressions #3558 described

2026-09-14 18:55:31 +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_confidence.py

fix(extract): give AST INFERRED edges a rubric confidence_score (#2813)

2026-08-18 16:02:02 +01:00

test_corrupt_graph_json.py

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test_cpp_nested_and_cli.py

fix(cpp): keep symbols for nested C++ types and C++/CLI sources (#2876)

2026-08-20 15:42:36 +01:00

test_cpp_objc_cross_file_calls.py

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test_cpp_preprocess.py

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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

fix(merge): respect C# type visibility across repos

2026-09-13 17:47:56 +01:00

test_cross_repo_member_calls.py

feat(merge): finish member calls across a repo boundary (#3152)

2026-09-02 14:58:01 +01:00

test_cross_repo_shared_types.py

test(merge): pin that a shared type links even when the declarations drift (#3007)

2026-08-24 14:12:53 +01:00

test_csharp_call_site_generic_args.py

fix(extract): collapse byte-identical duplicate edges at emission (#3251)

2026-09-05 01:18:59 +01:00

test_csharp_enum_members.py

feat(csharp): emit a node per enum member (#3063)

2026-08-25 15:45:06 +01:00

test_csharp_field_generic_args.py

fix(csharp): walk generic type arguments in field position

2026-08-21 16:50:25 +01:00

test_csharp_generic_callsites.py

fix(csharp): resolve unqualified generic call sites, Get<int>(...) (#3406)

2026-09-09 11:30:27 +01:00

test_csharp_interface_dispatch.py

feat(csharp): link interface methods to their single implementation (#3003)

2026-08-24 13:22:09 +01:00

test_csharp_member_calls.py

test(csharp): cover builtin-not-fabricated and struct primary-ctor (#2829)

2026-08-18 18:07:12 +01:00

test_csharp_member_nodes.py

feat(csharp): emit a member node per property (#3006)

2026-08-24 14:08:25 +01:00

test_csharp_object_creation.py

fix(csharp): emit calls edges for object creation expressions (#2997)

2026-08-24 13:17:23 +01:00

test_csharp_partial_classes.py

…

test_csharp_type_resolution.py

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test_dart.py

Add source_location to Dart extraction

2026-09-07 20:21:35 +01:00

test_dedup_remaps_hyperedges.py

test(dedup): pin chained-collapse and kept-single-member for hyperedge rewire (#2805)

2026-08-17 15:35:53 +01:00

test_dedup_survivor_richness.py

fix(dedup): pick the richer duplicate as survivor and keep the losers' fields (#3372)

2026-09-09 11:30:29 +01:00

test_dedup.py

Add negative control test for an ordinary ASCII path

2026-09-14 18:49:17 +01:00

test_definition_file_portability.py

fix(build): make definition_file portable, like its sibling source_file (#3223)

2026-09-02 03:05:59 +01:00

test_detect.py

fix: bare plural "tokens" in a prose file is no longer treated as a secret

2026-09-13 17:47:53 +01:00

test_devin.py

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test_dotnet.py

fix(razor): resolve @inject types across files (#3187)

2026-08-29 18:38:33 +01:00

test_duplicate_annotation_edges.py

fix(extract): collapse byte-identical duplicate edges at emission (#3251)

2026-09-05 01:18:59 +01:00

test_elixir_import_resolution.py

Add a regression test for a genuinely external module reference

2026-09-16 14:47:21 +01:00

test_evidence_binding.py

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test_explain_cli.py

Stop path::Symbol from shadowing a literal :: label

2026-09-11 23:58:31 +01:00

test_export_control_characters.py

fix(export): a control character in a label must not abort the export (#2897)

2026-08-20 16:09:00 +01:00

test_export_path_length.py

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test_export.py

test(export): lock non-ASCII round-trip byte-identity for field-order fix (#2582)

2026-08-18 22:27:27 +01:00

test_extract_cache_location.py

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test_extract_cli.py

fix(extract): scope fresh semantic results to dispatched files (#2926)

2026-08-21 19:21:20 +01:00

test_extract_code_only_cli.py

fix(extract): rescan code with --force --code-only (#3125)

2026-08-28 01:20:57 +01:00

test_extract.py

fix(extract): fall back to sequential when the process pool cannot start

2026-09-11 22:46:26 +01:00

test_extraction_spec_ids.py

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test_extractors_registry.py

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test_falkordb_integration.py

test(falkordb): skip when the port answers but is not FalkorDB

2026-08-27 20:20:16 +01:00

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_forwarding_review_findings.py

fix: preserve export cycles and legacy declaration facts

2026-09-05 21:55:33 +01:00

test_gemini_hook.py

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test_global_add_tag_inference.py

Never infer an empty repo tag for global add

2026-09-10 14:03:22 +01:00

test_global_graph.py

fix(build): offset community ids per input in merge-graphs (#3014)

2026-08-25 18:09:25 +01:00

test_go_builtin_call_targets.py

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test_go_qualified_resolution.py

test(go): cover method-level and all-exported case-only collisions (#2779)

2026-08-16 18:35:46 +01:00

test_god_nodes_cli.py

…

test_god_nodes_exclude_hubs.py

fix(analyze): god_nodes honours exclude_hubs_percentile (#3205)

2026-09-02 14:49:03 +01:00

test_google_workspace.py

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test_hollow_chunks_arm_shrink_guard.py

fix(extract): hollow, unparseable and omitting chunks count as incomplete (#3105)

2026-08-28 01:20:27 +01:00

test_home_sandbox.py

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test_hook_chain_survives_skip.py

fix(hooks): a graphify skip must not terminate the whole git hook (#2986)

2026-09-06 16:17:37 +01:00

test_hook_guard_token_match.py

fix(cli): hook-guard search detection matches executed commands, not prose (#3121)

2026-08-30 15:11:40 +01:00

test_hook_guard.py

fix(cli): hook-guard search detection matches executed commands, not prose (#3121)

2026-08-30 15:11:40 +01:00

test_hook_out_of_project_paths.py

fix(hooks): a driveless rooted path is not cwd-relative on Windows (#2795)

2026-08-19 14:05:58 +01:00

test_hook_strict.py

…

test_hooks.py

fix(hooks): resolve the output dir from GRAPHIFY_OUT in the sh gates, not a literal graphify-out/

2026-09-14 18:49:21 +01:00

test_hyperedge_member_shapes.py

…

test_hyperedge_roundtrip.py

…

test_hypergraph.py

test(export): cover many/empty id-less hyperedges; open 0.9.45 (#2775)

2026-08-16 18:28:53 +01:00

test_id_normalization_contract.py

fix(ids): make normalize_id caseless-stable via a casefold+NFKC fixpoint loop

2026-08-17 19:00:46 +01:00

test_ignore_file_encoding.py

fix(detect): decode a UTF-16-BOM ignore file instead of latin-1 garbage (#2798)

2026-08-17 15:40:19 +01:00

test_image_vision.py

test(claude): lock first-text-block (not concatenation) for the ThinkingBlock helper (#2697)

2026-08-18 22:20:19 +01:00

test_import_extension_resolution.py

…

test_import_self_loops.py

…

test_imported_export_forwarding.py

fix: resolve explicit named exports through imported bindings

2026-09-05 21:55:33 +01:00

test_incomplete_build_guard.py

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test_incremental_mtime_collision.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_catch_binding_shadow.py

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test_indirect_call_external_import_shadow.py

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test_indirect_call_for_of_binding_shadow.py

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test_indirect_call_function_expression_shadow.py

fix(js): also shadow generator function-expression bindings; lock .tsx coupling (#2752)

2026-08-15 20:11:13 +01:00

test_indirect_call_nested_closure_shadow.py

…

test_indirect_dispatch_assign_return.py

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test_indirect_dispatch_getattr.py

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test_indirect_dispatch.py

…

test_inferred_confidence_rubric.py

fix(extract): give AST INFERRED edges a rubric confidence_score (#2813)

2026-08-18 16:02:02 +01:00

test_ingest.py

fix(ingest): make memory-doc filenames unique so concurrent saves do not overwrite

2026-09-05 01:18:59 +01:00

test_inherited_field_receivers.py

fix(engine): resolve fields declared on a superclass for receivers in a subclass (#3151)

2026-08-29 16:14:47 +01:00

test_injection_sentinel_coverage.py

fix(llm): defang any <|token|> chat-template marker, not an enumerated few (#3183)

2026-08-30 15:11:24 +01:00

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

test(install): assert stale untouched platform still warns end-to-end (#2694)

2026-08-16 18:34:11 +01:00

test_install_version_warning.py

fix(install): actionable stale-skill warning; back up a diverged SKILL.md (#3144)

2026-08-30 15:11:40 +01:00

test_install.py

Use the replace fallback for skill install writes

2026-09-12 17:36:09 +01:00

test_issue_3405_python_resolution.py

Fix Python nested function resolution

2026-09-09 17:20:54 +01:00

test_issue_3472_source_file_collision.py

Fix same-file source path collision during merge

2026-09-10 22:44:39 +01:00

test_java_member_calls.py

fix(engine): resolve fields declared on a superclass for receivers in a subclass (#3151)

2026-08-29 16:14:47 +01:00

test_java_type_resolution.py

…

test_js_callback_calls.py

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test_js_destructured_export.py

Add a regression test for unexported require destructures

2026-09-14 18:49:19 +01:00

test_js_dynamic_import_affected.py

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test_js_dynamic_imports.py

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test_js_exported_fn_call_resolution.py

fix(js): resolve calls inside exported functions, incl. aliased imports (#3346)

2026-09-12 21:31:34 +01:00

test_js_exported_scalar_bindings.py

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test_js_import_resolution.py

fix(imports): pick workspace exports by importer platform, runtime before types

2026-09-12 21:31:35 +01:00

test_js_module_level_anonymous_calls.py

Add regression tests for module level anonymous calls

2026-09-13 17:47:55 +01:00

test_js_this_member_expressions.py

fix(js): keep this.X = function members in every enclosing-function form (#3408)

2026-09-09 11:30:28 +01:00

test_jsconfig_baseurl.py

fix(extract): invalidate tsconfig alias/baseUrl caches per run (#2917)

2026-08-21 16:49:55 +01:00

test_kotlin_grammar.py

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test_kotlin_object_literal.py

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test_label_retry.py

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test_labeling.py

test(labeling): keep the no-backend test hermetic against the claude-cli fallback

2026-09-10 22:45:31 +01:00

test_language_resolvers.py

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test_languages.py

fix: normalize definition_file on the watch and direct-extract paths (#3223)

2026-09-02 04:00:08 +01:00

test_llm_backends.py

fix: label via an installed claude CLI, and stop pinning a path that expires

2026-09-10 22:44:40 +01:00

test_llm_parser_reasoning.py

fix(llm): gate the reasoning-JSON winner on sanitized content, not raw value (#2882)

2026-08-20 15:44:56 +01:00

test_llm_parser.py

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test_long_path_hashing.py

…

test_loose_sibling_import_resolution.py

Fix loose sibling module import resolution

2026-09-09 17:20:56 +01:00

test_lua_import.py

test: cover bare require() imports edges for Lua (#3320)

2026-09-13 17:47:57 +01:00

test_manifest_ingest.py

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test_manifest_tomli_required.py

fix(manifest): require tomli on Py3.10 and fail loud when missing

2026-09-05 01:19:09 +01:00

test_markdown_code_spans.py

fix(markdown): honour dotted qualifiers and explicit relative cites in mention resolution

2026-09-16 14:50:54 +01:00

test_mcp_ingest.py

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test_merge_chunks_validation.py

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test_merge_graphs_cli.py

test(merge): pin same-order community-offset byte-reproducibility (#3014)

2026-08-25 18:09:58 +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): extract module-level static and const declarations

2026-09-10 22:44:38 +01:00

test_no_dedup_flag.py

test(extract): assert --no-dedup graph invariant, not just kwarg propagation (#2881)

2026-08-20 16:13:45 +01:00

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_category_interfaces.py

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test_objc_field_table_remap.py

fix(objc): remap the field->type table keys with the ids they hold (#3150)

2026-08-29 16:14:29 +01:00

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

test(obsidian): cover non-ASCII community tags and colour-group parity (#2862)

2026-08-19 14:05:58 +01:00

test_obsidian_vault_migration.py

fix(export): adopt a pre-manifest vault's own notes instead of orphaning them (#2863)

2026-08-21 19:22:21 +01:00

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_retry_cap.py

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test_ollama.py

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test_openai_custom_endpoint.py

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test_out_dir_evidence.py

fix(detect): probe every out subdirectory under an entry budget, not the first 20

2026-09-09 17:20:57 +01:00

test_oversized_document_slicing.py

fix(llm): bisect PDF slices on extracted text; reconcile splittable-PDF tests (#2906)

2026-08-21 16:57:29 +01:00

test_owned_type_sources.py

fix(resolution): require owned sources for type-use edges

2026-09-05 21:13:54 +01:00

test_package_json_subpath_imports.py

fix(js): resolve Node subpath imports via package.json imports

2026-09-07 19:02:18 +01:00

test_partial_cache.py

…

test_partial_extraction_warning.py

fix(extract): make the partial-parse warning actionable, and stop citing closed #2551 (#2788)

2026-08-19 14:05:58 +01:00

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

…

test_pdf_slicing.py

fix(llm): bisect PDF slices on extracted text; reconcile splittable-PDF tests (#2906)

2026-08-21 16:57:29 +01:00

test_pdf_token_estimate.py

fix(llm): estimate PDF tokens from the extracted text, not the container (#2903)

2026-08-21 16:50:44 +01:00

test_pg_introspect.py

fix(postgres): carry tree-sitter-sql in the postgres extra and surface grammar errors

2026-08-25 15:44:52 +01:00

test_phantom_cross_package_call.py

…

test_phantom_external_import.py

…

test_php_object_creation.py

test(php): escape namespace backslashes in object-creation fixtures (#3115)

2026-08-29 16:15:58 +01:00

test_php_type_resolution.py

Prefer the alias for a PHP use import edge's target

2026-09-09 17:20:56 +01:00

test_pipeline.py

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test_provider_registry.py

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test_prs.py

fix(mcp): prevent PR subprocess stdin hangs

2026-09-05 21:55:35 +01:00

test_prune_sweeps_orphans.py

test(build): pin shrink-guard safety and shared-stub survival for orphan sweep (#2807)

2026-08-17 15:33:34 +01:00

test_python_decorators.py

…

test_python_import_resolution.py

…

test_python_parse_memoization.py

perf(resolution): parse each Python file once across both resolution passes

2026-09-11 22:46:27 +01:00

test_python_underscore_resolution.py

Fix Python leading-underscore method/function id collision

2026-09-05 21:55:32 +01:00

test_query_cli.py

…

test_query_induced_edges.py

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test_query_mcp_direction.py

fix(serve): traverse the MCP query_graph undirected so a seed with no outgoing edges reaches its callers

2026-09-07 18:42:56 +01:00

test_query_names_its_graph.py

fix(query): name the graph the answer came from (#2789)

2026-08-18 22:36:42 +01:00

test_querylog.py

…

test_rationale.py

Fix module docstring extraction when a leading comment precedes it

2026-09-05 21:13:53 +01:00

test_read_hook.py

Add regression tests for the guard hook timeouts

2026-09-13 17:47:54 +01:00

test_reflect.py

…

test_relation_collapse_precedence.py

test(build): assert metadata survives demotion + unknown-relation is specific; open 0.9.46 (#2803)

2026-08-17 15:25:39 +01:00

test_replace_or_append_section.py

…

test_report_gap_thresholds.py

Update thin community tests for the corrected count

2026-09-14 18:49:20 +01:00

test_report.py

Surface unclassified files in GRAPH_REPORT.md

2026-09-12 17:36:10 +01:00

test_resolve_memoization.py

perf(resolution): memoize Path.resolve() across the symbol-resolution passes

2026-09-11 22:46:36 +01:00

test_ruby_resolution.py

fix: resolve inherited Ruby member calls

2026-09-16 14:43:05 +01:00

test_rust_self_member_calls.py

Refuse to pool methods across two unrelated same named types

2026-09-16 14:43:12 +01:00

test_scala_self_type.py

…

test_scip_ingest.py

…

test_search_hook.py

Add regression tests for the guard hook timeouts

2026-09-13 17:47:54 +01:00

test_security.py

…

test_semantic_cache_basename_recovery.py

Add regression test for dangling edge pruning consistency

2026-09-14 18:52:06 +01:00

test_semantic_cache_out_root.py

…

test_semantic_cleanup.py

…

test_semantic_fragment_sanitize.py

…

test_semantic_id_remap_root.py

…

test_semantic_similarity.py

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test_serve_http.py

Route get_node through the same resolver as get_neighbors

2026-08-29 18:38:05 +01:00

test_serve.py

fix: address Python 3.14 review findings

2026-09-12 21:35:25 +01:00

test_settings_merge.py

…

test_skill_version_warning.py

…

test_skillgen.py

chore(lock): sync uv.lock for the #3490 dependency-floor bumps; fix stale skillgen windows test

2026-09-12 21:49:56 +01:00

test_source_key_memoization.py

perf(resolution): memoize source-key resolution in the id-disambiguation pass

2026-09-11 22:46:36 +01:00

test_sourceless_call_targets.py

fix(extract): skip calls to sourceless stubs

2026-09-13 17:47:54 +01:00

test_src_layout_import_resolution.py

…

test_stale_prune.py

…

test_stat_index_husk.py

fix(cache): the atexit stat-index flush must not resurrect a deleted corpus (#2974)

2026-08-28 01:18:04 +01:00

test_stat_index_portability.py

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test_swift_builtin_noise.py

…

test_swift_computed_properties.py

…

test_swift_cross_file_calls.py

…

test_swift_import_resolution.py

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test_symbol_resolution.py

fix(extract): give AST INFERRED edges a rubric confidence_score (#2813)

2026-08-18 16:02:02 +01:00

test_terraform_modules.py

feat(terraform): resolve local module sources and directory topology

2026-09-15 18:01:35 +01:00

test_terraform.py

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test_trailing_newline_not_a_syntax_error.py

Add tests for newline char at EOF fix

2026-09-12 17:39:27 +01:00

test_transcribe.py

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test_tree_html.py

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test_ts_decorators.py

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test_ts_generators.py

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test_ts_import_require.py

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test_ts_import_type_arguments.py

test(ts): measure CPU time in the normalizer scaling test to de-flake it

2026-09-07 20:30:19 +01:00

test_ts_inheritance.py

fix(extract): emit inherits edge for JavaScript class extends (#1790)

2026-08-30 15:48:40 +01:00

test_ts_namespace.py

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test_ts_new_expression_calls.py

fix(ts): resolve new_expression constructor calls (#3116)

2026-08-27 20:57:16 +01:00

test_ts_parse_warning.py

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test_ts_receiver_member_calls.py

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test_type_only_import_cycles.py

fix(ts): type-only imports no longer manufacture Import Cycles (#3123)

2026-08-29 16:16:09 +01:00

test_typescript_enum_members.py

feat(typescript): emit a node per enum member (#3064)

2026-08-25 15:45:33 +01:00

test_typescript_module_extensions.py

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test_uninstall_scope.py

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test_unmapped_at_alias_resolution.py

fix: resolve unmapped @/ imports in JS projects

2026-09-06 16:17:38 +01:00

test_unverified_semantic_shrink.py

fix: protect against unverified semantic node loss (#3203)

2026-08-30 15:12:10 +01:00

test_validate.py

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test_vue_extraction.py

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test_walk_python_tree_iterative.py

perf(resolution): walk the Python tree iteratively, not via recursive yield-from

2026-09-11 22:46:26 +01:00

test_watch_manifest_location.py

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test_watch.py

fix: promote inherited Ruby call confidence

2026-09-15 18:03:12 +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

fix(wiki): say when a god-node relation group was truncated (#3127)

2026-08-30 15:11:23 +01:00

test_wiki.py

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test_word_count_cache.py

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test_zero_node_no_cache.py

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