Safi a26f24ef7b fix stale nodes persisting after file deletion when manifest uses absolute paths ...

prune_set in build_merge now includes relative-path variants of each deleted file
so manifest absolute paths (e.g. /home/user/corpus/module_b/utils.py) match graph
node source_file values (e.g. module_b/utils.py) regardless of OS or run context.
Fixes #1007.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

2026-05-26 14:53:36 +01:00

..

fixtures

add .NET project file support (.sln, .csproj, .fsproj, .vbproj, .razor, .cshtml)

2026-05-26 12:27:28 +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

conftest.py

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

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

test_affected_cli.py

feat: add v8 affected and import-resolution support

2026-05-22 13:24:54 +01:00

test_analyze.py

perf(analyze): reuse degrees for surprise scoring (#914)

2026-05-18 12:05:21 +01:00

test_astro_extraction.py

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

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

test_benchmark.py

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

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

test_build.py

fix stale nodes persisting after file deletion when manifest uses absolute paths

2026-05-26 14:53:36 +01:00

test_cache.py

Fix SSRF DNS rebinding TOCTOU and yt-dlp URL bypass (#591, #592)

2026-04-28 15:04:52 +01:00

test_callflow_html.py

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

2026-05-22 13:22:51 +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

feat(llm): split and retry chunks that hit max_completion_tokens truncation

2026-04-30 22:08:28 +10:00

test_claude_cli_backend.py

feat: add --backend claude-cli (routes through Claude Code, no API key needed) (#855)

2026-05-13 23:53:00 +01:00

test_claude_md.py

Fix PreToolUse hook for Claude Code v2.1.117+ (Glob|Grep → Bash matcher)

2026-04-28 00:56:54 +01:00

test_cli_export.py

fix(cli): reconstruct communities from per-node attribute when sidecar missing (#1001)

2026-05-24 20:35:21 +01:00

test_cluster.py

reduce graph update churn and stabilize community IDs

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

test_confidence.py

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

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

test_dedup.py

fix gitignore parent-exclusion rule (#882) and dedup false merges on short labels (#878)

2026-05-15 22:57:36 +01:00

test_detect.py

Fix wiki TypeError on null source_file and skip nested worktrees/ dirs (#1016, #1023)

2026-05-26 09:06:43 +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

add .NET project file support (.sln, .csproj, .fsproj, .vbproj, .razor, .cshtml)

2026-05-26 12:27:28 +01:00

test_explain_cli.py

fix path/explain arrow direction and bedrock CLI guard (#846, #849, #853)

2026-05-13 23:19:15 +01:00

test_export.py

Rate-limit backup_if_protected to one folder per day via content hash

2026-05-25 09:14:20 +01:00

test_extract_cli.py

Exit non-zero when all semantic-extraction chunks fail (#889)

2026-05-22 14:38:32 +01:00

test_extract.py

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

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

test_global_graph.py

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

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

test_google_workspace.py

Harden Google Workspace gws exports (#772)

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

test_hooks.py

test(hooks): cover old git hook path output (#910)

2026-05-18 12:04:49 +01:00

test_hypergraph.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_import_extension_resolution.py

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

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

test_incremental.py

Add incremental updates to graphify extract: semantic cache + build_merge + manifest

2026-05-04 18:07:02 +01:00

test_ingest.py

feat: cache, multi-language extraction, MCP, memory feedback

2026-04-04 18:56:38 +01:00

test_install_strings.py

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

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

test_install_upgrade.py

Stop telling assistants to read GRAPH_REPORT.md first (#580)

2026-05-15 20:17:52 -07:00

test_install.py

feat(install): add project-scoped skill installs (#931)

2026-05-22 14:38:35 +01:00

test_js_import_resolution.py

Fix: support array form of tsconfig extends (TypeScript 5.0) (#1017)

2026-05-26 09:17:14 +01:00

test_languages.py

add .NET project file support (.sln, .csproj, .fsproj, .vbproj, .razor, .cshtml)

2026-05-26 12:27:28 +01:00

test_llm_backends.py

fix Ollama num_ctx: derive from actual chunk size instead of hardcoding 131072 (#798)

2026-05-09 23:42:44 +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

feat: add v8 affected and import-resolution support

2026-05-22 13:24:54 +01:00

test_ollama.py

security hardening: F-002/F-005/F-007/F-008/F-009/F-010/F-016/F-031/F-035/F-038/PR747-NEW-2

2026-05-07 16:32:26 +01:00

test_pascal.py

add Pascal regex fallback - extraction works without tree-sitter-pascal

2026-05-09 15:52:17 +01:00

test_path_cli.py

fix path/explain arrow direction and bedrock CLI guard (#846, #849, #853)

2026-05-13 23:19:15 +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_prs.py

add graphify prs: graph-aware PR dashboard with triage, worktrees, conflict detection

2026-05-16 22:36:58 +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

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

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

test_rationale.py

Suppress autogenerated module docstrings from rationale extraction (#882)

2026-05-16 00:01:57 +01:00

test_report.py

Fix #664: filter thin communities from GRAPH_REPORT.md by default

2026-05-02 18:09:32 +01:00

test_scip_ingest.py

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

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

test_security.py

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

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

test_semantic_cleanup.py

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

2026-05-22 13:22:51 +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.py

Clarify Chinese query segmentation scope (#1026)

2026-05-26 12:24:04 +01:00

test_symbol_resolution.py

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

2026-05-22 13:22:51 +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_validate.py

feat: Claude Code skill, Obsidian vault, install, tests

2026-04-04 18:53:43 +01:00

test_watch.py

fix(watch): bypass shrink-guard when caller declared explicit deletions (#1000)

2026-05-24 20:35:19 +01:00

test_wiki.py

Fix wiki TypeError on null source_file and skip nested worktrees/ dirs (#1016, #1023)

2026-05-26 09:06:43 +01:00