safishamsi 36b5e770eb fix(detect): stop the sensitive-file filter from dropping topic docs and real source (#2106) ...

The heuristic over-matched and silently dropped legitimate files:
- prose `.md`/`.rst` whose topic slug ends in a keyword (privacy-tokens.md,
  token-economics.md) — only code was exempt, not prose;
- the unbounded Stage-2 `service.account` substring (regex `.` wildcard) matched
  real source (google/oauth2/service_account.py) and prose slugs.
It also MISSED real secrets (.npmrc, .pypirc, secring, .git-credentials, and
case variants on case-insensitive filesystems), which were being indexed.

Fix: move service_account/aws_credentials to the boundary-checked keyword path
(so real source is spared, downloaded key files still drop), add a prose-note
carve-out (multi-word slugs indexed, bare `secrets.md`/`token.md` still dropped),
tighten id_rsa with a left boundary, add the missed secret dotfiles + secring,
lowercase the dir/segment comparisons, and count multi-dot slugs as multi-word.
Net effect is stricter on real secrets and stops the false-positive data loss.

Traceability: `graphify extract` now names the files skipped as sensitive (not
just a count), so a wrongly-flagged file is visible.

2026-07-22 18:40:11 +01:00

..

fixtures

fix(sql): recover CREATE FUNCTION/PROCEDURE from tree-sitter ERROR nodes (#1910)

2026-07-15 10:58:57 +01:00

__init__.py

feat: core pipeline

2026-04-04 18:52:44 +01:00

bench_extract.py

feat: implement parallel AST extraction using ProcessPoolExecutor with benchmarking support

2026-05-02 12:54:08 +05:30

bench_query_scoring.py

test(serve): rebase #1900 test onto #1918 _score_query API; bench newline

2026-07-15 15:09:17 +01:00

conftest.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_affected_cli.py

fix(query): report real call-site lines + stop silent query truncation (benchmark)

2026-07-21 18:39:05 +01:00

test_affected_member_seed.py

feat(ruby/affected): mixes_in edges for include/extend/prepend + method-bound callers in affected (#1668, #1669)

2026-07-05 11:41:18 +01:00

test_agents_platform.py

feat(install): add cross-framework agents platform (+ skills alias)

2026-06-23 17:26:49 +01:00

test_analyze.py

fix(analyze): exclude rationale nodes from suggested-question gap count (#1768)

2026-07-11 11:52:12 +01:00

test_anthropic_custom_endpoint.py

feat: custom endpoints via OPENAI_BASE_URL/OPENAI_MODEL and ANTHROPIC_BASE_URL/ANTHROPIC_MODEL (#1273)

2026-06-16 01:41:15 +01:00

test_antigravity_install.py

write antigravity rules and workflows on project-scoped install

2026-06-02 23:48:54 +01:00

test_astro_extraction.py

feat(extract): add .astro support (#850)

2026-05-13 10:07:50 -07:00

test_atomic_writes.py

fix(io): route the remaining graph/manifest writers through the atomic helper (follow-up to #1952)

2026-07-16 23:48:07 +01:00

test_backend_extras.py

add anthropic extra and fix backend-missing hints for uv tool installs

2026-06-03 00:08:03 +01:00

test_benchmark.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_build_merge_hyperedges_and_prune.py

fix(build): form-insensitive prune + scan-root marker (#2012)

2026-07-20 13:29:54 +01:00

test_build.py

fix(build): ghost-merge keys on full source_file, not bare basename (#2068)

2026-07-21 13:03:34 +01:00

test_builtin_global_type_refs.py

test(extract): cover builtin static-call shape (Date.now()) for #1726

2026-07-08 12:09:40 +01:00

test_cache.py

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

test_callflow_html.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_cargo_introspect.py

fix(cargo): honor package = "..." rename when resolving internal deps (#1858)

2026-07-14 13:19:16 +01:00

test_case_sensitive_resolution.py

fix(extract): case-sensitive cross-file resolution in case-sensitive languages (#1581)

2026-07-01 15:09:42 +01:00

test_charmap_encoding.py

fix(llm): force UTF-8 encoding on _call_claude_cli subprocess + loud failure on chunk errors (#906)

2026-05-17 11:32:38 +01:00

test_chunking.py

fix(cache): don't promote truncated LLM chunks to the semantic cache as complete

2026-07-16 23:48:07 +01:00

test_cjs_module_extension.py

fix: treat .cjs (explicit CommonJS) as a code extension

2026-07-15 13:13:30 +01:00

test_claude_cli_backend.py

fix(llm): parse claude-cli structured_output, not the prose result field (follow-up to #2095)

2026-07-22 15:57:54 +01:00

test_claude_md.py

fix(install): fire the search nudge on Claude Code's Grep tool, not just Bash (#1986)

2026-07-18 19:07:16 +01:00

test_cli_broken_pipe.py

fix(export): coerce non-scalar attrs in graphml; harden pipe-close flush

2026-07-12 23:57:16 +01:00

test_cli_export.py

test(cli): graph.json node ids are portable across checkout paths (#1789)

2026-07-11 16:31:10 +01:00

test_cluster.py

reduce graph update churn and stabilize community IDs

2026-05-12 02:23:51 +03:00

test_codebuddy.py

fix(install): fire the search nudge on Claude Code's Grep tool, not just Bash (#1986)

2026-07-18 19:07:16 +01:00

test_community_hub_labels.py

fix(cluster): detect stale community labels on cluster-only re-cluster

2026-07-01 11:52:50 +01:00

test_confidence.py

v2: confidence scores on INFERRED edges, avg shown in report

2026-04-06 16:06:31 +01:00

test_corrupt_graph_json.py

test(build): add regression tests for corrupt graph.json (#1537)

2026-07-01 10:49:43 +01:00

test_cpp_objc_cross_file_calls.py

feat(extract): cross-file member-call resolution for C++ and ObjC (#1547, #1556)

2026-06-30 18:30:05 +01:00

test_cpp_preprocess.py

harden ollama metadata egress and cpp path handling (F3, F5)

2026-06-02 22:23:15 +01:00

test_cross_extension_reexport_self_cycle.py

fix(resolution): repoint cross-extension re-exports without leaking an absolute path (#1814)

2026-07-18 12:04:23 +01:00

test_cross_language_call_resolution.py

fix(extract): never bind a cross-file call to a definition in another language family

2026-07-08 01:16:58 +01:00

test_csharp_member_calls.py

test(csharp): chained call off new X(...) resolves (#1770)

2026-07-10 21:57:16 +01:00

test_csharp_type_resolution.py

feat(csharp): namespace-aware cross-file type resolution (#1562)

2026-06-30 19:32:10 +01:00

test_dart.py

feat(extract): SystemVerilog class-level extraction; Dart with-clause mixin fix

2026-06-11 19:52:56 +03:00

test_dedup.py

fix(dedup): order-independent gap-fill, source_file gate, _origin/None handling (follow-up to #2102)

2026-07-22 16:11:15 +01:00

test_detect.py

fix(detect): stop the sensitive-file filter from dropping topic docs and real source (#2106)

2026-07-22 18:40:11 +01:00

test_devin.py

feat: add Devin CLI support (graphify devin install/uninstall) (#1020)

2026-05-26 09:17:18 +01:00

test_dotnet.py

fix(extract): close residual absolute-path/username leaks (#1899)

2026-07-14 23:42:06 +01:00

test_evidence_binding.py

fix(llm): move the unverifiable-node flag to a real, consumed field (follow-up to #1949)

2026-07-17 00:09:02 +01:00

test_explain_cli.py

fix: group cut connections by file on explain for high-degree nodes

2026-07-22 15:27:07 +01:00

test_export.py

fix(extract): fail closed on malformed existing graph + honor walk_errors (follow-up to #1951)

2026-07-16 23:42:47 +01:00

test_extract_cache_location.py

fix(cache): stat-index must follow the cache location, not the key anchor

2026-07-13 10:29:26 +01:00

test_extract_cli.py

fix(extract): initialize detection for pathless Postgres

2026-07-20 11:31:36 +01:00

test_extract_code_only_cli.py

fix(detect): stop the sensitive-file filter from dropping topic docs and real source (#2106)

2026-07-22 18:40:11 +01:00

test_extract.py

test(extract): external-alias negative + warm-cache coverage for #2082 (follow-up to #2093)

2026-07-22 15:40:00 +01:00

test_extraction_spec_ids.py

fix(ids): node IDs include the full repo-relative path (#1504, #1509)

2026-06-28 16:57:00 +01:00

test_extractors_registry.py

test(extractors): guard facade + registry identity for the per-language split (#1721)

2026-07-09 13:22:36 +01:00

test_falkordb_integration.py

feat: add FalkorDB export backend (#1175)

2026-06-07 15:03:49 +03:00

test_file_label_disambiguation.py

fix(cli): disambiguate file labels on the --no-cluster extract path too (#2032)

2026-07-20 16:35:14 +01:00

test_file_node_id_spec.py

fix(ids): node IDs include the full repo-relative path (#1504, #1509)

2026-06-28 16:57:00 +01:00

test_file_slice.py

Slice oversized text documents so the whole file is extracted (#1369)

2026-06-18 01:55:56 +01:00

test_gemini_hook.py

Fix: port the Gemini CLI BeforeTool graph-nudge hook to be shell-agnostic too (#522)

2026-07-06 16:43:21 +01:00

test_global_graph.py

fix(global-graph): rewire edges to deduplicated external nodes (#1250)

2026-06-11 09:36:38 +02:00

test_god_nodes_cli.py

fix(cli): wire god-nodes subcommand + accept --output alias on extract (#2004)

2026-07-20 15:35:40 +01:00

test_google_workspace.py

Harden Google Workspace gws exports (#772)

2026-05-07 20:07:57 +01:00

test_hook_guard.py

test: rigorous edge cases for the hook-guard subcommand (#522)

2026-07-06 16:49:31 +01:00

test_hook_strict.py

fix(install): fire the search nudge on Claude Code's Grep tool, not just Bash (#1986)

2026-07-18 19:07:16 +01:00

test_hooks.py

Fix spurious hooksPath warning and register graph.json merge driver

2026-07-15 00:41:36 +01:00

test_hypergraph.py

fix(hyperedge): accept members/node_ids alias keys for the member list (#1561)

2026-06-30 16:58:23 +01:00

test_id_normalization_contract.py

Unify node-ID normalization into a single source of truth (#1378)

2026-06-18 22:55:44 +01:00

test_image_vision.py

Contain symlinked extraction inputs

2026-07-02 22:29:32 +01:00

test_import_extension_resolution.py

fix(extract): apply resolver fixups to JS/TS dynamic_import handler

2026-05-05 00:07:50 +02:00

test_import_self_loops.py

fix: drop collapsed import self-loops

2026-07-20 11:29:22 +01:00

test_incomplete_build_guard.py

fix(extract): fail closed on malformed existing graph + honor walk_errors (follow-up to #1951)

2026-07-16 23:42:47 +01:00

test_incremental.py

fix(update): prune edges owned by a re-extracted file (#1521)

2026-06-28 19:29:51 +01:00

test_indirect_dispatch_assign_return.py

feat(extract): capture assignment/return indirect_call edges (#1566 slice 2)

2026-06-30 23:26:13 +01:00

test_indirect_dispatch_getattr.py

feat(extract): capture getattr(obj, "name") indirect_call edges (#1566 slice 3)

2026-07-01 10:30:47 +01:00

test_indirect_dispatch.py

fix(extract): cross-file indirect_call survives id relativization (0.9.4 regression)

2026-07-01 11:43:05 +01:00

test_ingest.py

feat: self-improving work-memory — save-result outcomes + graphify reflect (#1441)

2026-06-24 11:43:13 +01:00

test_install_references.py

fix: four production bugs — Windows crashes, ghost-merge collision, version probe

2026-06-13 15:13:23 +01:00

test_install_roundtrip.py

feat(skills): progressive-disclosure split for all platforms (generator + drift fence) (#1121)

2026-06-02 20:48:13 +01:00

test_install_strings.py

Fix: port the Gemini CLI BeforeTool graph-nudge hook to be shell-agnostic too (#522)

2026-07-06 16:43:21 +01:00

test_install_upgrade.py

Fix: make Claude Code / Codebuddy PreToolUse graph-nudge hooks work on Windows (#522)

2026-07-06 16:38:42 +01:00

test_install.py

fix(install): uninstall must not delete a user's ### graphify H3 section (#2062)

2026-07-21 12:40:49 +01:00

test_java_member_calls.py

fix(extract): resolve Java member calls by receiver type (#1696)

2026-07-10 02:11:36 +01:00

test_java_type_resolution.py

fix(extract): resolve Java cross-module type references by import (#1744)

2026-07-09 10:44:50 +01:00

test_js_import_resolution.py

fix(extract): don't guess an ambiguous barrel re-export (follow-up to #2034)

2026-07-20 11:41:44 +01:00

test_label_retry.py

Adaptive split-and-retry for community labeling on parse failure (#1280, #1278)

2026-06-18 22:50:52 +01:00

test_labeling.py

fix(label): --no-label placeholders no longer permanently suppress real labels (#2073)

2026-07-21 12:59:10 +01:00

test_language_resolvers.py

feat(ruby): type-aware member-call resolution via a resolver framework (#1499)

2026-06-29 09:40:22 +01:00

test_languages.py

fix(extract): nested types get a contains edge from the enclosing type (#2040)

2026-07-20 15:40:32 +01:00

test_llm_backends.py

fix(llm): fall back to OLLAMA_HOST when OLLAMA_BASE_URL is unset

2026-07-20 11:29:22 +01:00

test_llm_parser.py

fix(claude-cli): deliver extraction instructions in the user turn

2026-07-02 22:29:30 +01:00

test_long_path_hashing.py

fix(detect): incremental correctness for Office sources + long paths, cache word counts (#1649, #1655, #1656)

2026-07-04 22:12:47 +01:00

test_manifest_ingest.py

Parse package manifests into canonical package nodes + depends_on edges (#1377)

2026-06-19 10:25:09 +01:00

test_mcp_ingest.py

feat: MCP config extractor (.mcp.json, claude_desktop_config.json, mcp.json)

2026-05-26 20:16:41 +01:00

test_merge_chunks_validation.py

fix(merge-chunks): fail when no chunk validates

2026-07-17 10:54:07 +01:00

test_merge_graphs_cli.py

fix(merge-graphs): give each input a distinct repo tag so same-stem nodes don't collapse (#1729)

2026-07-08 12:45:08 +01:00

test_minhash.py

perf/fix: replace datasketch with pure-numpy MinHash; memoize detect ignore checks

2026-06-10 15:50:38 +01:00

test_multigraph_compat.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_multigraph_diagnostics.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_multilang.py

fix(sql): recover CREATE FUNCTION/PROCEDURE from tree-sitter ERROR nodes (#1910)

2026-07-15 10:58:57 +01:00

test_obsidian_dangling_member.py

fix(export): guard to_canvas against dangling community members (#1236 follow-up)

2026-07-03 18:34:41 +01:00

test_obsidian_filename_cap.py

cap obsidian/canvas filenames to avoid ENAMETOOLONG on long labels (fixes #1094)

2026-05-31 16:41:18 +01:00

test_office_incremental.py

fix(detect): incremental correctness for Office sources + long paths, cache word counts (#1649, #1655, #1656)

2026-07-04 22:12:47 +01:00

test_office_limits.py

tighten F2 and F3 from review: bounded decompression, ollama DNS + clean error

2026-06-02 22:50:33 +01:00

test_ollama_retry_cap.py

Fix: cap Ollama client-side retries so a hung request cannot multiply the stall (#1686)

2026-07-06 12:44:47 +01:00

test_ollama.py

tighten F2 and F3 from review: bounded decompression, ollama DNS + clean error

2026-06-02 22:50:33 +01:00

test_openai_custom_endpoint.py

feat: custom endpoints via OPENAI_BASE_URL/OPENAI_MODEL and ANTHROPIC_BASE_URL/ANTHROPIC_MODEL (#1273)

2026-06-16 01:41:15 +01:00

test_partial_cache.py

fix(cache): mark files partial on empty-parse truncation (follow-up to #1950)

2026-07-17 00:02:15 +01:00

test_pascal_call_scoping.py

fix(extract): scope Pascal/Delphi call resolution + resolve inherited calls across files (#1739)

2026-07-09 00:32:21 +01:00

test_pascal_resolution.py

fix(extract): scope Pascal/Delphi call resolution + resolve inherited calls across files (#1739)

2026-07-09 00:32:21 +01:00

test_pascal.py

fix: surface silently-skipped dirs in enumeration + dedup Pascal edges

2026-07-09 01:06:02 +01:00

test_path_cli.py

fix(path): deterministic route + honest edge relation, not fabricated calls (#2074)

2026-07-21 12:54:58 +01:00

test_paths.py

fix(resolve): test mocks no longer erase the real cross-file call graph (#1553)

2026-06-30 16:59:16 +01:00

test_pg_introspect.py

fix(pg_introspect): emit FK DDL before function stubs so unparseable routines can't drop references edges (#1854)

2026-07-16 16:36:49 +01:00

test_phantom_cross_package_call.py

fix(extract): gate JS/TS cross-file calls on import evidence to kill phantom cross-package edges (#1659)

2026-07-04 21:22:39 +01:00

test_phantom_external_import.py

fix: harden semantic extraction and kill phantom import edges (#1631, #1638, #1632)

2026-07-04 03:12:23 +01:00

test_php_type_resolution.py

fix: preserve semantic layer, stamp hyperedges, PHP namespaces, ignore diagnostic (#1925 #1920 #1923 #1922)

2026-07-15 19:51:53 +01:00

test_pipeline.py

v0.4.15: VS Code Copilot Chat, OpenCode/Gemini Windows fixes, .mjs/.ejs, macOS watch, god_nodes degree rename

2026-04-15 23:08:43 +01:00

test_provider_registry.py

validate custom-provider base_url and gate project-local providers (F1)

2026-06-02 22:16:58 +01:00

test_prs.py

fix(prs): decode gh/git/claude output as UTF-8, not the Windows cp1252 codec

2026-07-18 12:03:47 +01:00

test_python_import_resolution.py

feat: add cross-language semantic contexts for Python, JS/TS, C#, and Java (#996)

2026-05-24 20:38:10 +01:00

test_query_cli.py

fix: preserve calls edge direction in graphify query output

2026-07-21 21:45:53 +01:00

test_querylog.py

fix(querylog): make the query log opt-in, off by default (#1797)

2026-07-12 10:36:00 +01:00

test_rationale.py

feat: extract rationale comments + ADR/RFC doc references from JS/TS

2026-07-06 00:45:51 +01:00

test_read_hook.py

Fix: make Claude Code / Codebuddy PreToolUse graph-nudge hooks work on Windows (#522)

2026-07-06 16:38:42 +01:00

test_reflect.py

fix(reflect): layout-ordered source resolution for overlay staleness (#1558)

2026-06-30 12:57:33 +01:00

test_replace_or_append_section.py

Fix: exact-match section heading in _replace_or_append_section to prevent CLAUDE.md data loss (#1688)

2026-07-06 12:36:12 +01:00

test_report.py

fix(report): don't emit dangling [[_COMMUNITY_*]] wikilinks by default (#1712)

2026-07-07 10:57:52 +01:00

test_ruby_resolution.py

fix(extract): route .rake files to the Ruby extractor + resolution (#1784)

2026-07-11 11:31:47 +01:00

test_scip_ingest.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

test_search_hook.py

fix(install): fire the search nudge on Claude Code's Grep tool, not just Bash (#1986)

2026-07-18 19:07:16 +01:00

test_security.py

test: guard to_html/sanitize_label against null source_file/label (#1775)

2026-07-10 20:24:25 +01:00

test_semantic_cache_out_root.py

fix(cache): anchor semantic cache writes to cache_root so --out round-trips (#1990, #1991)

2026-07-18 19:09:53 +01:00

test_semantic_cleanup.py

fix(merge-chunks): validate untrusted subagent chunk JSON before merging

2026-07-16 23:36:49 +01:00

test_semantic_fragment_sanitize.py

fix: harden semantic extraction and kill phantom import edges (#1631, #1638, #1632)

2026-07-04 03:12:23 +01:00

test_semantic_id_remap_root.py

fix(build): make _semantic_id_remap idempotent to stop id accretion (#1917)

2026-07-15 15:14:34 +01:00

test_semantic_similarity.py

v2: semantic similarity edges, scored higher in surprising connections

2026-04-06 16:06:31 +01:00

test_serve_http.py

feat(serve): optional project_path for multi-project MCP serving

2026-07-02 12:11:51 +01:00

test_serve.py

test(serve): guard + direction tests for dangling _src/_tgt (follow-up to #2080)

2026-07-21 21:46:42 +01:00

test_skill_version_warning.py

fix(cli): make skill-version warning direction-aware (#1568)

2026-06-30 23:15:52 +01:00

test_skillgen.py

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

test_src_layout_import_resolution.py

fix(extract): harden #2072 src-layout resolution (adversarial-review fixes)

2026-07-21 14:22:50 +01:00

test_swift_cross_file_calls.py

fix(swift): resolve calls on a singleton cached into a local var (#1604)

2026-07-02 11:46:22 +01:00

test_swift_import_resolution.py

Collapse Swift module imports to one shared node

2026-06-16 03:06:43 +01:00

test_symbol_resolution.py

fix(resolve): test mocks no longer erase the real cross-file call graph (#1553)

2026-06-30 16:59:16 +01:00

test_terraform.py

revert: remove importorskip now that uv.lock includes tree-sitter-hcl

2026-06-05 21:46:25 +01:00

test_transcribe.py

Remove Anthropic API call from transcribe.py - agent generates Whisper prompt itself

2026-04-10 15:55:22 +01:00

test_ts_decorators.py

fix(extract): emit reference edges for TS/JS decorators

2026-07-02 22:38:29 +01:00

test_ts_generators.py

fix(extract): extract TS/JS generator functions as nodes

2026-07-02 22:38:28 +01:00

test_ts_import_require.py

fix: harden semantic extraction and kill phantom import edges (#1631, #1638, #1632)

2026-07-04 03:12:23 +01:00

test_ts_inheritance.py

capture TS interface-extends and same-file class heritage (fixes #1095)

2026-05-31 16:47:52 +01:00

test_ts_namespace.py

fix(extract): emit a node for TS namespace / module containers

2026-07-02 22:38:29 +01:00

test_ts_receiver_member_calls.py

feat(extract): TS/JS member calls on local new-binding + typed-param receivers (#1630)

2026-07-03 16:03:18 +01:00

test_typescript_module_extensions.py

fix(extract): recognize uppercase TypeScript

2026-07-14 23:32:02 +01:00

test_validate.py

Fix: validate_extraction crashes on non-hashable node id / edge endpoint

2026-06-24 08:54:11 +01:00

test_vue_extraction.py

fix(extract): parse .vue SFC <script> with the right grammar (#1468)

2026-06-26 10:20:53 +01:00

test_watch.py

fix(watch): don't evict remote-source nodes after URL slash-collapse (#2051 follow-up)

2026-07-20 13:57:12 +01:00

test_wheel_packaging.py

feat(install): add cross-framework agents platform (+ skills alias)

2026-06-23 17:26:49 +01:00

test_wiki.py

fix(wiki): portable relative markdown links so navigation works outside Obsidian (#1444)

2026-06-27 10:19:15 +01:00

test_word_count_cache.py

fix(cache): key file_hash stat-index memo by salt, not absolute path (#1989)

2026-07-18 12:03:34 +01:00

test_zero_node_no_cache.py

fix(extract): don't cache zero-node results; warn on empty source files (#1666)

2026-07-05 10:33:07 +01:00