bump to v0.6.2

CHANGELOG.md

@@ -2,6 +2,23 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.6.2 (2026-05-01)
+
+- Fix: Kimi K2.6 reasoning mode consumed entire token budget leaving `content` empty — thinking now disabled on Moonshot calls so graphs actually populate (#623)
+- Fix: `graphify update` / `graphify watch` never persisted the manifest, so every subsequent `--update` re-extracted all files — manifest now saved after each rebuild (#621)
+- Fix: inline comments in `.graphifyignore` (e.g. `vendor/ # legacy`) now stripped correctly — whitespace + `#` suffix is treated as a comment, `path#hash.py` preserved (#605)
+- Fix: `graphify query "FunctionName"` now returns the exact matching node first instead of high-degree hub modules hijacking the output — 100-point exact-match bonus + seeds render before BFS expansion (#638)
+- Fix: concurrent AST extractors raced on a shared `.tmp` cache file — each writer now gets a unique tempfile via `mkstemp`, eliminating cache corruption under parallel extraction (#589)
+- Fix: `_clone_repo` branch names starting with `-` could be interpreted as git flags — validation added, `--` separator inserted before positional args (#589)
+- Fix: replaced `html2text` (GPL-3.0) with `markdownify` (MIT) — removes the only copyleft dependency from a MIT project (#586)
+- Fix: `--update` re-extracted files whose mtime was bumped by sync tools (Obsidian, Nextcloud) without content changes — manifest now stores content hash alongside mtime; mtime bump triggers an MD5 check before re-extraction (#593)
+- Feat: R language support — `.r` files classified as code and processed via LLM semantic extraction (#617)
+- Feat: extensionless shell scripts now detected via shebang (`#!/bin/bash`, `#!/usr/bin/env python3`, etc.) and included as code (#619)
+- Fix: cross-language INFERRED `calls` edges (e.g. Python→TypeScript name collision) no longer appear as top surprising connections in GRAPH_REPORT.md (#630)
+- Fix: `cluster-only` CLI silently flipped directed graphs to undirected — `directed` flag now read from graph.json and preserved through re-clustering (#590)
+- Fix: Windows UNC / extended-length paths (`\\?\C:\...`) now normalize to consistent cache keys (#629)
+- Fix: `.graphifyignore` negation patterns (`!src/lib/secrets.ts`) now work — full last-match-wins evaluation with `!` un-ignore support (#628)
+
 ## 0.6.1 (2026-05-01)
 
 - Fix: `.graphifyignore` discovery now uses correct gitignore semantics — outer rules are loaded first so inner (closer) rules always win via last-match-wins, matching standard gitignore behavior (#643)

README.md

@@ -49,7 +49,7 @@ dist/
 *.generated.py
 ```
 
-Same syntax as `.gitignore`. You can keep a single `.graphifyignore` at your repo root — patterns work correctly even when graphify is run on a subfolder. Discovery never crosses a VCS boundary (`.git`, `.hg`, etc.), so sibling projects in a shared workspace don't leak rules into each other. Without a VCS root, only the scan folder's own `.graphifyignore` applies.
+Same syntax as `.gitignore` — including `!` negation patterns to re-include specific files. You can keep a single `.graphifyignore` at your repo root — patterns work correctly even when graphify is run on a subfolder. Discovery never crosses a VCS boundary (`.git`, `.hg`, etc.), so sibling projects in a shared workspace don't leak rules into each other. Without a VCS root, only the scan folder's own `.graphifyignore` applies. Inline comments are supported: `vendor/ # legacy deps`.
 
 ## How it works
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.6.1"
+version = "0.6.2"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, Gemini CLI, Aider, OpenClaw, Factory Droid, Trae, Hermes, Kiro, Google Antigravity) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }