CHANGELOG.md

Changelog

Full release notes with details on each version: GitHub Releases

0.4.11 (2026-04-13)

• Fix: graphify query no longer crashes with ValueError on MultiGraph graphs — G.edges[u, v] replaced with G[u][v] + MultiGraph guard (#305)
• Fix: graphify query no longer crashes with AttributeError: 'NoneType' has no attribute 'lower' when a node has a null source_file (#307)
• Fix: MCP server launched from a different directory now correctly derives the graphify-out base from the absolute path provided, instead of CWD (#309)
• Fix: .graphifyignore patterns from a parent directory now fire correctly when graphify is run on a subfolder — patterns are matched against paths relative to both the scan root and the .graphifyignore's anchor directory (#303)

0.4.10 (2026-04-13)

• Fix: graphify install --platform cursor no longer crashes — passes Path(".") to _cursor_install (#281)
• Fix: _agents_uninstall now only removes the OpenCode plugin when uninstalling the opencode platform — other platforms were incorrectly having their OpenCode plugin stripped (#276)
• Fix: misleading comment in query --graph path handler removed (#278)
• Fix: skill-codex.md — wait → wait_agent (correct Codex tool name) (#273)
• Add: svg = ["matplotlib"] optional extra in pyproject.toml; matplotlib added to [all] extra (#288)
• Fix: graspologic dependency now has python_version < '3.13' env marker in leiden and all extras — prevents install failures on Python 3.13+ (#290)
• Add: Dart/Flutter support — .dart files extracted via regex (classes, mixins, functions, imports); added to CODE_EXTENSIONS (#292)
• Add: norm_label field written at build time in to_json() for diacritic-insensitive search; _score_nodes and _find_node in serve.py use norm_label with Unicode NFKD normalization fallback (#293)
• Add: Hermes Agent platform support — graphify hermes install writes skill to ~/.hermes/skills/graphify/SKILL.md and AGENTS.md (#251)
• Add: PHP extractor now captures static property access (Foo::$bar) as uses_static_prop edges (#234)
• Add: PHP extractor now captures config() helper calls as uses_config edges pointing to the first config key segment (#236)
• Add: PHP extractor now captures service container bindings (bind, singleton, scoped, instance) as bound_to edges (#238)
• Add: PHP extractor now captures $listen / $subscribe event listener arrays as listened_by edges (#240)
• Add: prune_dangling_edges() utility in export.py — removes edges whose source/target is not in the node set (#294)
• Fix: Antigravity install injects YAML frontmatter into skill file for native tool discovery; rules now include MCP navigation hint; prints MCP config snippet (#268)
• Fix: Windows hook tests now use platform-aware assertions instead of POSIX executable bit checks (#279)
• Add: CLI commands path, explain, add, watch, update, cluster-only now work as bare terminal commands (not just AI skill invocations) — documented in --help output (#277)

0.4.8 (2026-04-12)

• Fix: platform skill files (aider, codex, opencode, claw, droid, copilot, windows) no longer contain Claude-specific language — references to "Claude" as the AI model replaced with platform-agnostic wording (#272)

0.4.7 (2026-04-12)

• Fix: watch semantic edge preservation was always empty — graph.json uses links key but code read edges (#269)
• Fix: graphify claw install now writes to .openclaw/ (correct OpenClaw directory) instead of .claw/ (#208)
• Add: Blade template support — @include, <livewire:> components, and wire:click bindings extracted from .blade.php files (#242)
• Docs: WSL/Linux MCP setup note — package name is graphifyy, use .venv/bin/python3 in .mcp.json (#250)

0.4.6 (2026-04-12)

• Add: Google Antigravity support — graphify antigravity install writes .agent/rules/graphify.md (always-on rules) and .agent/workflows/graphify.md (/graphify slash command) (#203, #199, #53)

0.4.5 (2026-04-12)

• Fix: MCP server no longer crashes with ValidationError on blank lines sent between JSON messages by some clients (#201)

0.4.4 (2026-04-12)

• Fix: watch now preserves INFERRED/AMBIGUOUS edges (code↔doc rationale links) across rebuilds — previously all cross-type edges were dropped (#261)
• Fix: Codex hook no longer emits permissionDecision:allow which codex-cli 0.120.0 rejects (#249)
• Fix: Common lockfiles (package-lock.json, yarn.lock, Cargo.lock, etc.) are now skipped during detection, preventing token drain on large JS/Rust/Python projects (#266)

0.4.3 (2026-04-12)

• Fix: JS/TS relative imports now resolve to full-path node IDs — previously all imports_from edges were silently dropped on large TypeScript codebases (#256)
• Fix: Python relative imports (from .foo import bar) now resolve correctly to full-path node IDs (#256)
• Fix: watch --rebuild_code now merges fresh AST with existing semantic nodes from docs/papers instead of overwriting them (#253)
• Fix: Windows hooks now fall back to python if python3 is not found; exits cleanly if neither has graphify installed (#244)
• Fix: surprising_connections / suggest_questions no longer crash with KeyError on stale _src/_tgt edge hints after node merges (#226)
• Add: .vue and .svelte files now recognized as code and included in extraction (#254)

0.4.2 (2026-04-11)

• Fix: same-basename files in different directories produced colliding node IDs — now uses full path (#211)
• Fix: edges using from/to keys instead of source/target were silently dropped (#216)
• Fix: empty graphs (no edges) crashed to_html with ZeroDivisionError (#217)
• Fix: post-commit hook skipped .tsx, .jsx, and other valid code extensions due to stale allowlist (#222)
• Fix: NetworkX ≤3.1 serialises edges as links — now accepted alongside edges (#212)
• Fix: version warning fired during install/uninstall and duplicated on shared paths (#220)
• Fix: all file IO now uses encoding="utf-8" — prevents crashes on Windows with CJK or emoji labels; hook writes use newline="\n" to prevent CRLF shebang breakage (#204)
• Fix: Obsidian export — node labels ending in .md produced .md.md filenames; GRAPH_REPORT.md now links to community hub files so vault stays in one connected component (#221)

0.4.1 (2026-04-10)

• Fix: collect_files() in extract.py now respects .graphifyignore — previously ignored patterns, causing thousands of unwanted files (e.g. node_modules/) to be scanned (#188)
• Fix: skill.md Step B2 now explicitly requires subagent_type="general-purpose" — using Explore type silently dropped extraction results since it is read-only and cannot write chunk files (#195)
• Fix: Step B3 now warns when chunk files are missing from disk instead of silently skipping them

0.4.0 (2026-04-10)

• Branch: v4 — video and audio corpus support
• Add: drop .mp4, .mp3, .wav, .mov, .webm, .m4a, .ogg, .mkv, .avi, .m4v files into any corpus and graphify transcribes them locally with faster-whisper before extraction
• Add: YouTube and URL download via yt-dlp — /graphify add https://youtube.com/... downloads audio-only and feeds it through the same Whisper pipeline
• Add: domain-aware Whisper prompts — the coding agent reads god nodes from the corpus and writes a one-sentence domain hint for Whisper itself, no separate API call
• Add: graphify-out/transcripts/ cache — transcripts cached by filename; YouTube URLs cached by hash so re-runs skip already-transcribed files
• Requires: pip install 'graphifyy[video]' for faster-whisper and yt-dlp

0.3.29 (2026-04-10)

• Add: video and audio corpus support — drop .mp4, .mp3, .wav, .mov, .webm, .m4a, .ogg, .mkv, .avi, .m4v files into any corpus and graphify transcribes them with faster-whisper before extraction
• Add: YouTube and URL video download — pass a YouTube link (or any video URL) to /graphify add <url> and yt-dlp downloads audio-only, which is then transcribed and added to the corpus automatically
• Add: domain-aware Whisper prompts — god nodes from non-video files are used to build a one-sentence domain hint for Whisper via a cheap Haiku call, improving transcript accuracy on technical content
• Add: graphify-out/transcripts/ cache — transcripts are cached by filename so re-runs skip already-transcribed files; URLs cached by hash
• Requires: pip install 'graphifyy[video]' for faster-whisper + yt-dlp

0.3.28 (2026-04-10)

• Fix: hook installers (Claude Code, Codex, Gemini CLI) now always remove and reinstall the hook on re-run — users upgrading from old versions no longer get stuck with a broken hook format (#182)
• Fix: rationale node labels no longer contain bare \r characters on Windows/WSL CRLF files — breaks Obsidian export was silently producing invalid filenames (#176)
• Fix: skill-windows.md now includes --wiki, --obsidian-dir, and --directed which were missing vs the main skill (#177)

0.3.27 (2026-04-10)

• Fix: graphify install --platform gemini now also copies the skill file to ~/.gemini/skills/graphify/SKILL.md so the /graphify trigger works in Gemini CLI (#174)

0.3.26 (2026-04-10)

• Fix: MCP server no longer uses a circular path validation when loading a graph outside cwd — now validates the path exists and ends in .json instead of checking containment within its own parent directory (security fix)

0.3.25 (2026-04-09)

• Fix: graphify install --platform gemini now routes to gemini_install() instead of erroring — gemini was missing from _PLATFORM_CONFIG (#171)
• Fix: graphify install --platform cursor now routes to _cursor_install() the same way (#171)
• Fix: serve.py validate_graph_path now passes base=Path(graph_path).resolve().parent so MCP server works when graph is outside cwd (#170)
• Fix: MCP call_tool() handler now wraps dispatch in try/except — exceptions in tool handlers return graceful error strings instead of crashing the stdio loop (#163)
• Fix: _load_graphifyignore now walks parent directories up to the .git boundary, matching .gitignore discovery behavior — subdirectory scans now inherit root ignore patterns (#168)
• Add: Aider platform support — graphify install --platform aider copies skill to ~/.aider/graphify/SKILL.md; graphify aider install/uninstall writes AGENTS.md rules (#74)
• Add: GitHub Copilot CLI platform support — graphify install --platform copilot copies skill to ~/.copilot/skills/graphify/SKILL.md; graphify copilot install/uninstall for skill management (#134)
• Add: --directed flag — build_from_json() and build() now accept directed=True to produce a DiGraph preserving edge direction (source→target); cluster() converts to undirected internally for Leiden; graph_diff edge key handles directed graphs correctly (#125)
• Add: Frontmatter-aware cache for Markdown files — .md files hash only the body below YAML frontmatter, so metadata-only changes (reviewed, status, tags) no longer invalidate the cache (#131)

0.3.24 (2026-04-09)

• Fix: graphify codex install (and opencode) no longer exits early when AGENTS.md already has the graphify section — partial installs with a missing .codex/hooks.json can now recover on re-run (#153)

0.3.23 (2026-04-09)

• Add: Gemini CLI support — graphify gemini install writes a GEMINI.md section and a BeforeTool hook in .gemini/settings.json that fires before file-read tool calls (#105)
• Add: sponsor nudge at pipeline completion — all skill files now print a one-line sponsor link after a fresh build, not on --update runs

0.3.22 (2026-04-09)

• Add: Cursor support — graphify cursor install writes .cursor/rules/graphify.mdc with alwaysApply: true so the graph context is always included; graphify cursor uninstall removes it (#137)
• Fix: _rebuild_code() KeyError — detected[FileType.CODE] corrected to detected['files']['code'] matching detect()'s actual return shape; was silently breaking git hooks on every commit (#148)
• Fix: to_json() crash on NetworkX 3.2.x — node_link_data(G, edges="links") now falls back to node_link_data(G) on older NetworkX, same shim already used for node_link_graph (#149)
• Fix: README clarifies graphifyy is the only official PyPI package — other graphify* packages are not affiliated (#129)

0.3.21 (2026-04-09)

• Fix: Codex PreToolUse hook now places systemMessage at the top level of the output JSON instead of inside hookSpecificOutput — matches the strict schema enforced by codex-cli 0.118.0+ which uses additionalProperties: false (#138)
• Fix: git hooks now use #!/bin/sh instead of #!/bin/bash — Git for Windows ships sh.exe not bash, so hooks were silently skipped on Windows (#140)

0.3.20 (2026-04-09)

• Fix: XSS in interactive HTML graph — node labels, file types, community names, source files, and edge relations now HTML-escaped before innerHTML injection; neighbor link onclick uses JSON.stringify instead of raw string interpolation
• Add: OpenCode tool.execute.before plugin — graphify opencode install now writes .opencode/plugins/graphify.js and registers it in opencode.json, firing the graph reminder before bash calls (equivalent to Claude Code's PreToolUse hook) (#71)
• Fix: AST-resolved call edges now carry confidence=EXTRACTED, weight=1.0 instead of INFERRED/0.8 — tree-sitter call resolution is deterministic, not probabilistic (#127)
• Fix: tree-sitter>=0.23.0 now pinned in dependencies and _check_tree_sitter_version() guard added — stale environments now get a clear RuntimeError with upgrade instructions instead of a cryptic TypeError deep in the AST pipeline (#89)

0.3.19 (2026-04-09)

• Fix: install step now tries plain pip install before falling back to --break-system-packages — Homebrew and PEP 668 managed environments no longer risk environment corruption (#126)

0.3.18 (2026-04-09)

• Fix: --watch mode now respects .graphifyignore — _rebuild_code was calling collect_files() directly instead of detect(), bypassing ignore patterns (#120)
• Fix: Codex PreToolUse hook now uses systemMessage instead of additionalContext — Codex does not support additionalContext and was returning an error (#121)
• Fix: Trae link corrected from trae.com to trae.ai in README, README.zh-CN.md, README.ja-JP.md, README.ko-KR.md (#122)
• Docs: Korean README added (README.ko-KR.md) (#112)
• Refactor: save_query_result inline Python blocks in all 6 skill files replaced with graphify save-result CLI command — shorter, maintainable, less tokens for LLM (#114)
• Add: graphify save-result CLI subcommand — saves Q&A results to memory dir without inline Python
• Fix: HTML graph click detection now uses hover-tracking (hoveredNodeId) — more reliable than vis.js click params on small/dense nodes (#82)
• Fix: mkdir -p graphify-out now runs before writing .graphify_python in skill.md — prevents write failure on first run; .graphify_python no longer deleted in Step 9 cleanup across all skill files so follow-up commands keep their interpreter (#93)
• Fix: skill-trae.md added to pyproject.toml package-data — Trae users no longer hit ModuleNotFoundError after pip install (#102)
• Fix: analyze.py and watch.py now import extension sets from detect.py instead of local copies — Swift, Lua, Zig, PowerShell, Elixir, JSX, Julia, Objective-C files no longer misclassified as documents (#109)
• Refactor: dead build_graph() function removed from cluster.py (#109)

0.3.17 (2026-04-08)

• Add: Julia (.jl) support — modules, structs, abstract types, functions, short functions, using/import, call edges, inherits edges via tree-sitter-julia (#98)
• Fix: Semantic extraction chunks now group files by directory so related artifacts land in the same chunk, reducing missed cross-chunk relationships (#65)
• Fix: tree-sitter>=0.21 now pinned in dependencies — prevents silent empty AST output when older tree-sitter is installed with newer language bindings (#52)
• Add: Progress output every 100 files during AST extraction so large projects don't appear to hang (#52)

0.3.16 (2026-04-08)

• Fix: graphify query, serve, and benchmark now work on NetworkX < 3.4 — version-safe shim for node_link_graph() at all call sites (#95)
• Fix: .jsx files now detected and extracted via the JS extractor — added to CODE_EXTENSIONS and _DISPATCH (#94)
• Fix: .graphify_python no longer deleted in Step 9 cleanup across all 6 skill files — pipx users no longer hit ModuleNotFoundError on follow-up commands (#92)

0.3.15 (2026-04-08)

• Feat: Trae and Trae CN platform support (graphify install --platform trae / trae-cn)
• Fix: skill-droid.md was missing from PyPI package data — Factory Droid users couldn't install the skill
• Fix: XSS in HTML legend — community labels now HTML-escaped before innerHTML injection
• Fix: Shebang allowlist validation in hooks.py and all 6 skill files — prevents metacharacter injection from malicious binaries
• Fix: louvain_communities() kwargs now inspected at runtime for cross-version NetworkX compatibility
• Fix: pipx installs now detected correctly in git hooks (reads shebang from graphify binary)
• Fix: graspologic ANSI escape codes no longer corrupt PowerShell 5.1 scroll buffer
• Docs: Japanese README added
• Docs: graph.json + LLM workflow example added to README
• Docs: Codex PreToolUse hook now documented in platform table

0.3.14 (2026-04-08)

• Fix: graphify codex install now also writes a PreToolUse hook to .codex/hooks.json so the graph reminder fires before every Bash tool call (#86)
• Fix: --update now prunes ghost nodes from deleted files before merging new extraction (#51)

0.3.13 (2026-04-08)

• Fix: PreToolUse hook now outputs additionalContext JSON so Claude actually sees the graph reminder before Glob/Grep calls (#83)
• Fix: Go AST method receivers and type declarations now use package directory scope, eliminating disconnected duplicate type nodes across files in the same package (#85)
• Fix: PDFs inside Xcode asset catalogs (.imageset, .xcassets) are no longer misclassified as academic papers (#52)
• Fix: _resolve_cross_file_imports is now guarded with if py_paths and wrapped in try/except so a Python parser crash can't abort extraction for non-Python files (#52)
• Fix: Skill intermediate files (.graphify_*.json) now live in graphify-out/ instead of project root, preventing git pollution (#81)

0.3.12 (2026-04-07)

• Fix: sanitize_label was double-encoding HTML entities in the interactive graph (< instead of <) — removed html.escape() from sanitize_label; callers that inject directly into HTML now call html.escape() themselves (#66)
• Fix: --wiki flag missing from skill.md usage table (#55)

0.3.11 (2026-04-07)

• Fix: Louvain fallback hangs indefinitely on large sparse graphs — added max_level=10, threshold=1e-4 to prevent infinite loops while preserving community quality (#48)

0.3.10 (2026-04-07)

• Fix: Windows UnicodeEncodeError during graphify install — replaced arrow character with -> in all print statements (#47)
• Add: skill version staleness check — warns when installed skill is older than the current package, across all platforms (#46)

0.3.9 (2026-04-07)

• Add: follow_symlinks parameter to detect() and collect_files() — opt-in symlink following with circular symlink cycle detection (#33)
• Fix: watch.py now uses collect_files() instead of manual rglob loop for consistency
• Docs: Codex uses $graphify . not /graphify . (#36)
• Test: 5 new symlink tests (367 total)

0.3.8 (2026-04-07)

• Add: C# inheritance and interface implementation extraction — base_list now emits inherits edges for both simple (identifier) and generic (generic_name) base types (#45)
• Add: graphify query "<question>" CLI command — BFS/DFS traversal of graph.json without needing Claude Code skill (--dfs, --budget N, --graph <path> flags)
• Test: 2 new C# inheritance tests (362 total)

0.3.7 (2026-04-07)

• Add: Objective-C support (.m, .mm) — @interface, @implementation, @protocol, method declarations, #import directives, message-expression call edges
• Add: --obsidian-dir <path> flag — write Obsidian vault to a custom directory instead of graphify-out/obsidian
• Fix: semantic cache was only saving 4/17 files — relative paths from subagents now resolved against corpus root before existence check
• Fix: 75 validation warnings per run for file_type: "rationale" — added "rationale" to VALID_FILE_TYPES
• Test: 6 Objective-C tests; .m/.mm added to test_collect_files_from_dir supported set (360 total)

0.3.0 (2026-04-06)

• Add: multi-platform support — Codex (skill-codex.md), OpenCode (skill-opencode.md), OpenClaw (skill-claw.md)
• Add: graphify install --platform <codex|opencode|claw> routes skill to correct config directory
• Add: graphify codex install / opencode install / claw install — writes AGENTS.md for always-on graph-first behaviour
• Add: graphify claude uninstall / codex uninstall / opencode uninstall / claw uninstall
• Add: MIT license
• Fix: build() was silently dropping hyperedges when merging multiple extractions
• Refactor: extract.py 2527 → 1588 lines — replaced 12 copy-pasted language extractors with LanguageConfig dataclass + _extract_generic()
• Docs: clustering is graph-topology-based (no embeddings) — explained in README
• Docs: all missing flags documented (--cluster-only, --no-viz, --neo4j-push, query --dfs, query --budget, add --author, add --contributor)

0.2.2 (2026-04-06)

• Add: graphify claude install — writes graphify section to local CLAUDE.md + PreToolUse hook in .claude/settings.json
• Add: graphify claude uninstall — removes section and hook
• Add: graphify hook install — installs post-commit and post-checkout git hooks (platform-agnostic)
• Add: graphify hook uninstall / hook status
• Add: graphify benchmark CLI command
• Fix: node deduplication documented at all three layers

0.1.8 (2026-04-05)

• Fix: follow-up questions now check for wiki first (graphify-out/wiki/index.md) before falling back to graph.json
• Fix: --update now auto-regenerates wiki if graphify-out/wiki/ exists
• Fix: community articles show truncation notice ("... and N more nodes") when > 25 nodes
• UX: pipeline completion message now lists all available flags and commands so users know what graphify can do

0.1.7 (2026-04-05)

• Add: --wiki flag — generates Wikipedia-style agent-crawlable wiki from the graph (index.md + community articles + god node articles)
• Add: graphify/wiki.py module with to_wiki() — cross-community wikilinks, cohesion scores, audit trail, navigation footer
• Add: 14 wiki tests (245 total)
• Fix: follow-up question example code now correctly splits node labels by _ to extract verb prefixes (previous version used def/fn prefix matching which always returned zero results)

0.1.6 (2026-04-05)

• Fix: follow-up questions after pipeline now answered from graph.json, not by re-exploring the directory (was 25 tool calls / 1m30s; now instant)
• Skill: added "Answering Follow-up Questions" section with graph query patterns

0.1.5 (2026-04-05)

• Perf: semantic extraction chunks 12-15 → 20-25 files (fewer subagent round trips)
• Perf: code-only corpora skip semantic dispatch entirely (AST handles it)
• Perf: print timing estimate before extraction so the wait feels intentional
• Fix: 5 skill gaps - --graphml in Usage table, --update manifest timing, query/path/explain graph existence check, --no-viz clarity
• Refactor: dead imports removed (shutil, sys, inline os); _node_community_map() helper replaces 8 copy-pasted dict comprehensions; to_html() split into _html_styles() + _html_script(); serve.py call_tool() if/elif chain replaced with dispatch table
• Test: end-to-end pipeline integration test (detect → extract → build → cluster → analyze → report → export)

0.1.4 (2026-04-05)

• Replace pyvis with custom vis.js HTML renderer - node size by degree, click-to-inspect panel with clickable neighbors, search box, community filter, physics clustering
• HTML graph generated by default on every run (no flag needed)
• Token reduction benchmark auto-runs after every pipeline on corpora over 5,000 words
• Fix: 292 edge warnings per run eliminated - stdlib/external edges now silently skipped
• Fix: build() cross-extraction edges were silently dropped - now merged before assembly
• Fix: pip install graphify → pip install graphifyy in skill Step 1 (critical install bug)
• Add: --graphml flag implemented in skill pipeline (was documented but not wired up)
• Remove: pyvis dependency, dead lib/ folder, misplaced eval reports from tests/
• Add: 5 HTML renderer tests (223 total)

0.1.3 (2026-04-04)

• Fix: pyproject.toml structure - requires-python and dependencies were incorrectly placed under [project.urls]
• Add: GitHub repository and issues URLs to PyPI page
• Add: keywords for PyPI search discoverability
• Docs: README clarifies Claude Code requirement, temporary PyPI name, worked examples footnote

0.1.1 (2026-04-04)

• Add: CI badge to README (GitHub Actions, Python 3.10 + 3.12)
• Add: ARCHITECTURE.md - pipeline overview, module table, extraction schema, how to add a language
• Add: SECURITY.md - threat model, mitigations, vulnerability reporting
• Add: worked/ directory with eval reports (karpathy-repos 71.5x benchmark, httpx, mixed-corpus)
• Fix: pytest not found in CI - added explicit pip install pytest step
• Fix: README test count (163 → 212), language table, worked examples links
• Docs: README reframed as Claude Code skill; Karpathy problem → graphify answer framing

0.1.0 (2026-04-03)

Initial release.

• 13-language AST extraction via tree-sitter (Python, JS, TS, Go, Rust, Java, C, C++, Ruby, C#, Kotlin, Scala, PHP)
• Leiden community detection via graspologic with oversized community splitting
• SHA256 semantic cache - warm re-runs skip unchanged files
• MCP stdio server - query_graph, get_node, get_neighbors, shortest_path, god_nodes
• Memory feedback loop - Q&A results saved to graphify-out/memory/, extracted on --update
• Obsidian vault export with wikilinks, community tags, Canvas layout
• Security module - URL validation, safe fetch with size cap, path guards, label sanitisation
• graphify install CLI - copies skill to ~/.claude/skills/ and registers in CLAUDE.md
• Parallel subagent extraction for docs, papers, and images