Release 0.9.9

Fixes since 0.9.8: explain punctuated-label matching (#1704); surface code files
with no AST extractor instead of dropping them silently (#1689); consistent
AST-extraction progress denominator (#1693); no dangling Obsidian wikilinks in
GRAPH_REPORT.md by default (#1712); MATLAB .m no longer force-parsed by the
Objective-C grammar (#1702); corrected the /graphify usage comment in the skill
files (#1681); surface unclassified files (Dockerfile/Makefile/...) instead of
vanishing (#1692).

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

Author: safishamsi

CHANGELOG.md

@@ -2,6 +2,16 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.9.9 (2026-07-07)
+
+- Fix: `graphify explain` resolves an exactly-typed punctuated label symmetrically against `norm_label` (#1704). The search term tokenized on `\w+` ("blockStream.ts" -> "blockstream ts", space where the '.' was) while a node's stored `norm_label` keeps punctuation ("blockstream.ts"). The verbatim case was already rescued by the tokenized-label tier, but that broke if a node's `label` and `norm_label` diverged; a punctuation-preserving `norm_query` is now matched against `norm_label` across the exact/prefix/substring tiers (and fed to the trigram prefilter), so it is robust by construction.
+- Fix: code files with no AST extractor are surfaced instead of silently dropped (#1689, thanks for the precise root-cause). `.r`/`.R` (also `.ejs`, `.ets`) are in `CODE_EXTENSIONS` so they are counted as code, but there is no extractor for them, so they produced zero nodes with no warning. `extract` now prints a grouped warning ("N file(s) are classified as code but graphify has no AST extractor ...: .r (17)"). Adding a real `tree-sitter-r` extractor remains a follow-up.
+- Fix: the AST-extraction progress line keeps a consistent denominator to the end (#1693). Intermediate lines counted against `len(uncached_work)` but the final line switched to `total_files` (which includes cached hits and no-extractor files), so on a large corpus the count appeared to jump upward right after 99%. Both the parallel and sequential final lines now use the `uncached_work` denominator.
+- Fix: `GRAPH_REPORT.md` no longer emits dangling `[[_COMMUNITY_*]]` Obsidian wikilinks by default (#1712). The `_COMMUNITY_*.md` notes those links target are only created by the opt-in `--obsidian` export, and the report is written at build time before any export, so on a default run every link dangled (spawning phantom nodes in a vault's graph view, literal brackets elsewhere). The Community Hubs section now renders as plain text by default; the wikilink form is behind an `obsidian=True` opt-in.
+- Fix: `.m` files are no longer force-parsed by the Objective-C grammar when they are MATLAB (#1702, thanks @catalystdream for the diagnosis). `.m` is shared by Objective-C and MATLAB, but the dispatch routed every `.m` to `extract_objc`, which turned real MATLAB into garbage nodes/edges. `.m` is now content-sniffed like `.h`: a genuine Objective-C `.m` (with `@implementation`/`@interface`/`@import`/`#import`) still routes to `extract_objc`; a MATLAB `.m` gets no extractor and is surfaced by the #1689 warning rather than mis-parsed. `.mm` is unchanged (unambiguously Objective-C++). A real `tree-sitter-matlab` extractor remains a follow-up.
+- Fix: the `/graphify` usage comment in the skill files no longer claims a bare `/graphify` produces an Obsidian vault by default (#1681, thanks for the audit). It now reads "full pipeline on current directory (HTML viz; add `--obsidian` for a vault)", matching Step 6. Fixed at the skillgen source so every generated `skill-*.md` variant carries the corrected comment.
+- Feat: files graphify sees but cannot classify are surfaced instead of vanishing (#1692). Extensionless, non-shebang project files (Dockerfile, Gemfile, Makefile, Rakefile, LICENSE, ...) and unsupported extensions previously left no trace at all. `detect` now collects them into an `unclassified` list, and `graphify extract` reports "N file(s) not classified (no supported extension or shebang), skipped: ...". Actually extracting Dockerfile/Makefile-style content remains a follow-up.
+
 ## 0.9.8 (2026-07-06)
 
 - Fix: the Claude Code / Codebuddy `PreToolUse` and Gemini CLI `BeforeTool` graph-nudge hooks now work on Windows (#522). The hooks were inline POSIX bash (`case/esac`, `[ -f ]`, single-quoted `echo`), which Windows cmd.exe/PowerShell cannot parse — so on Windows the hook failed silently, no "run `graphify query` before grepping/reading raw files" context was injected, and users had to invoke `/graphify` by hand. The detection logic (grep-command match, source-file extension match, skip-if-under-output-dir, graph-exists check) moved into a shell-agnostic `graphify hook-guard <search|read>` subcommand invoked via the absolute exe path (the same pattern the codex hook already uses), so the hook parses and runs identically on Windows, macOS, and Linux. Behavior on macOS/Linux is unchanged (byte-identical nudge payload); the graph path now also honors `GRAPHIFY_OUT`. The Gemini `BeforeTool` hook got the same treatment (`graphify hook-guard gemini`), which also removes its dependency on a bare `python` being on PATH. Codex stays a no-op there because Codex Desktop rejects `additionalContext`.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.9.8"
+version = "0.9.9"
 description = "AI coding assistant skill (Claude Code, CodeBuddy, Codex, OpenCode, Kilo Code, Cursor, Gemini CLI, Aider, OpenClaw, Factory Droid, Trae, Hermes, Kiro, Pi, Devin CLI, Google Antigravity) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }