• 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).