v0.9.9

graphify 0.9.9 — reliability + honesty round on top of the 0.9.8 Windows-hooks release.

Highlights: explain resolves punctuated labels; code files with no AST extractor (R, .ejs, .ets) and unclassifiable files (Dockerfile/Makefile) are now surfaced instead of silently dropped; MATLAB .m no longer garbage-parses through the Objective-C grammar; GRAPH_REPORT.md no longer emits dangling Obsidian wikilinks by default.

Install: `uv tool install "graphifyy==0.9.9"` or `pip install graphifyy==0.9.9`

## Changelog


- 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.