safishamsiandClaude Opus 4.8 137dcf23fe fix(extract): incremental --no-cluster merges instead of overwriting the graph (#2169) ...

An incremental `extract --no-cluster` wrote only the changed files over
graph.json with no merge, dropping every node/edge owned by an unchanged
file; and the id-canonicalization pass only learned batch files, so the
changed file's cross-file edges kept absolute-path target ids and
dangled. The raw path now merges the existing graph forward with the same
replace/prune semantics as the clustered path (new merge_raw_extraction
helper in build.py, shared loader), refuses to overwrite a corrupt
existing graph, and the remap pass now also learns in-root edge
target_file paths (existence-gated) so cross-file targets canonicalize.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-07-25 22:53:43 +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

…

bench_extract.py

…

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

test: sandbox HOME for the whole suite so installers can't touch real config (#2168)

2026-07-25 18:02:33 +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

…

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

…

test_antigravity_install.py

…

test_astro_extraction.py

…

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

…

test_benchmark.py

…

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

…

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

…

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

…

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

…

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

…

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

…

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): honor ignore files saved with a UTF-8 BOM (#2163)

2026-07-24 23:47:25 +01:00

test_devin.py

…

test_dotnet.py

fix(extract): bound the XAML code-behind .cs scan so it can't hang

2026-07-22 19:31:19 +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): cover calls into a ${VAR}-sourced bash lib (follow-up to #2139)

2026-07-24 23:47:25 +01:00

test_extraction_spec_ids.py

…

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

…

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

…

test_file_slice.py

…

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

…

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

…

test_home_sandbox.py

test: sandbox HOME for the whole suite so installers can't touch real config (#2168)

2026-07-25 18:02:33 +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(hooks): match the post-checkout log prefix in the timeout fallback

2026-07-24 23:37:14 +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

…

test_image_vision.py

Contain symlinked extraction inputs

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

test_import_extension_resolution.py

…

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): incremental --no-cluster merges instead of overwriting the graph (#2169)

2026-07-25 22:53:43 +01:00

test_incremental.py

fix(extract): incremental --no-cluster merges instead of overwriting the graph (#2169)

2026-07-25 22:53:43 +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

test(extract): cover cross-file class-ref indirect_call suppression (#2137)

2026-07-24 23:37:14 +01:00

test_ingest.py

…

test_install_references.py

…

test_install_roundtrip.py

…

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_jsconfig_baseurl.py

test(resolution): cover jsconfig/baseUrl module resolution (#2153)

2026-07-25 15:44:50 +01:00

test_label_retry.py

…

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

…

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

…

test_mcp_ingest.py

…

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

…

test_multigraph_compat.py

…

test_multigraph_diagnostics.py

…

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

…

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

…

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

…

test_openai_custom_endpoint.py

…

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

…

test_provider_registry.py

…

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_decorators.py

test(extract): cover Python decorator reference edges (#2154)

2026-07-25 15:44:50 +01:00

test_python_import_resolution.py

…

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

…

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

…

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_settings_merge.py

fix(install): never clobber an unparseable settings file; back up before write (#2167)

2026-07-25 22:53:43 +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_builtin_noise.py

fix(extract,analyze): filter Swift/Foundation/SwiftUI builtins from resolution and god-node ranking (#2147)

2026-07-25 15:44:50 +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

…

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

…

test_transcribe.py

…

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

…

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

…

test_vue_extraction.py

…

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

…

test_wiki.py

…

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