v0.9.41

Correctness, determinism, and data-integrity release — a large batch of community-contributed fixes.

- Fix: `graphify update` refuses to overwrite the graph with a shrunken one when the shrink was caused by an extractor failure this run, instead of silently replacing good data (#2663, thanks @ousamabenyounes); a genuine deletion still shrinks the graph.
- Fix: a JS/TS `catch` binding passed as a call argument no longer fabricates an `indirect_call` edge to an unrelated same-named callable (thanks @imagineers-tyler); completes the 0.9.38/0.9.40 arrow-parameter fixes (#2568).
- Fix: `Cargo.toml` is recognized as a package manifest (#2434, thanks @ousamabenyounes), minting a canonical package node plus `depends_on` edges.
- Fix: an explicitly-passed scan root is no longer excluded by an unanchored pattern in a parent-directory `.gitignore` (#2468, thanks @hopstreax).
- Fix: the API extraction prompt now instructs backends to capture the per-node `rationale` attribute, matching the skill path (#2482, thanks @hopstreax). Invalidates cached semantic chunks, which re-extract on the next run.
- Fix: `source_file` is canonicalized to POSIX separators, so relative inputs on Windows no longer produce non-portable node ids (#2627, thanks @rajarshidattapy).
- Fix: a warm cache hit no longer re-anchors a CWD-relative `source_file` to a ghost path when the working directory differs from the graph root (#2632, thanks @rajarshidattapy).
- Fix: the wiki/obsidian audit trail counts each incident edge once instead of double-counting intra-community edges (#2635, thanks @rajarshidattapy).
- Fix: C# members inside a `#if ... #endif` preprocessor block are extracted and attached to their class (#2634, thanks @rohit-jsfreaky).
- Fix: `query` no longer prints the truncation banner when no nodes were actually cut (#2601, thanks @ousamabenyounes); a genuine node truncation still warns.
- Fix: a PHP `use` import written with a leading-backslash / fully-qualified prefix now resolves to its target definition (#2661, thanks @ousamabenyounes).
- Fix: an unresolved local JS/TS import (to a file absent from the scan) emits a stable, portable `ref` target id instead of a per-checkout absolute-path slug (#2457, thanks @rohit-jsfreaky).
- Fix: `graphify benchmark` no longer crashes on a node whose label is `None` (#2674, thanks @Arthuro0103).