v0.9.47

- Fix: extraction now bisects a file chunk on timeout instead of failing the whole chunk, so one slow file no longer drops its chunk-mates from the graph; recognized timeouts (subprocess, SDK, and botocore read/connect) route through the same bounded split-and-merge path as context-window-exceeded errors, and a single unsplittable file that times out is left unstamped and retried next run (#2866, thanks @hopstreax).
- Fix: the cache no longer collapses symlinks when keying files, so a symlink alias and its target get distinct identities and one no longer displaces the other from the graph on a warm cache; the detect-layer containment guard that resolves paths to block symlink escape is unchanged (#2832, thanks @oleksii-tumanov).
- Fix: `graphify extract --out <dir>` no longer writes converted Office/Google-Workspace sidecars back into the scanned source tree; sidecar writes go through the cache root while the content hash stays anchored to the scan root, so a read-only or pinned checkout stays clean (#2787, thanks @hopstreax).
- Fix: the git-hook out-of-project read guard no longer misclassifies a rooted-but-driveless path (`\foo\bar`) as cwd-relative on Windows, where such a path resolves against the current drive root and is actually outside the project; POSIX behaviour is unchanged (#2795, thanks @abhay-codes07).
- Fix: the partial-parse warning no longer ends with a hardcoded citation to the closed Kotlin-specific issue #2551 (which misdirected reporters of unrelated failures); it now reports the surviving symbol count so a total-loss file reads differently from a partially-recovered one (#2788, thanks @abhay-codes07).
- Fix: Obsidian export now keeps non-ASCII letters (Hangul, CJK, Cyrillic, accented Latin) in community tags instead of collapsing every non-Latin community to the same underscore tag, and the graph-view colour groups query the identical tag so colours match again (#2862, thanks @josh-leung-KR).
- Feature: JavaScript/TypeScript factory functions that assign callable members to a local object literal (`const api = {}; api.foo = fn`) now keep those members in the graph — the API object is modeled beneath its factory and the assigned functions attach as methods, including arrow-function assignments and their intra-factory call edges. The owner is minted only for identifiers proven to be object-literal bindings in the enclosing function, so arbitrary receivers do not reintroduce the phantom-owner flood, and the factory's `contains` edge is emitted once no matter how many methods hang off the object (#2745, thanks @rajanpanth).
- Fix: `graph.json` field order is now stable across a read-rebuild round-trip, so re-running `graphify update` on an unchanged graph produces a byte-identical file instead of reshuffling node and link keys (#2582, thanks @C0KERNEL).
- Fix: `graphify query` now names the graph it opened and its node count at the head of the answer (relative to the CWD when the graph is underneath it, absolute otherwise), so a query run from a parent project no longer silently answers from the wrong corpus with no indication which graph was used (#2789, thanks @abhay-codes07).
- Fix: the `claude` backend no longer crashes with `AttributeError: 'ThinkingBlock'` when an extended-thinking response leads with a thinking block; the first text block is read instead (#2697, thanks @mdshzb04).
- Fix: `graphify update` / `save_manifest` no longer rewrites `manifest.json` timestamps on a no-op run, so `graphify-out/` stops showing as dirty (and stops producing a trailing graph commit) when nothing changed; a genuine change still updates and persists (#2838, thanks @hopstreax).
- Fix: a C# 12 primary constructor's parameters are now walked, so `class Svc(IRepo repo)` emits the `references` edge to `IRepo` and calls through `repo` resolve — previously the class silently dropped its dependency; built-in and type-parameter types are not fabricated (#2829, thanks @brobl2008).
- Fix: AST-derived INFERRED edges now carry a rubric `confidence_score` keyed to the relation (`uses` 0.95, `indirect_call`/unresolved cross-file `calls` 0.85) instead of landing at the rubric-forbidden 0.5 or a flat 0.8; the INFERRED default moves 0.5→0.55 so every score-less INFERRED edge is on the discrete rubric set (#2813, thanks @abhay-codes07).
- Fix: a legacy `graph.json` that stored a numeric edge `confidence` (from a pre-enum version) no longer warns once per edge on every incremental reload; the numeric value is normalized to the `INFERRED` tag with the original float preserved in `confidence_score` (thanks @Trantor-develops).