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Requirement or Bug
Security auditfails onmainand every open PR: new advisories were published on 2026-11-09 (dompurify critical; undici, zod, electron, vue-i18n/@intlify, body-parser, follow-redirects, systeminformation, @azure/msal-node high; others moderate/low).Bug Reproduction Steps
pnpm auditonmainreports the advisories above.Root Cause
New upstream advisories against locked versions. Separately, the
pre-pushhook ran the test suite withGIT_DIR/GIT_INDEX_FILEexported, and tests that spawngitin temp dirs (tower, nix-hash) wrote commits and config into the real repository. Fundamental fix for both.Code Changes
pnpm.overrides: raise floors, each capped to its current major line (dompurify, undici, vue-i18n, @intlify/*, systeminformation, @azure/msal-node, body-parser, follow-redirects, fastify, fast-uri 3 and 4, serialize-javascript, qs, ip-address, vitest/@vitest/mocker~4.1.12, @hono/node-server^2.1.3).glob@>=9 <14.0.2to^14.0.2,minimatch@>=7 <11.0.1to^11.0.1(build and dev tooling only), andzod@3to^4.6.6for jimp (smoke-tested: blit, resize, crop, PNG encode).electron43.5.0 to 43.8.7 (desktop); zod catalog 4.4.3 to 4.6.7.auditConfig.ignoreGhsasgainsGHSA-gcqx-w48m-w2h4(deepmerge, no patched release; reached only via shadcn in the VS Code app).vitest.config.tsdeletes the repo-locatingGIT_*variables before workers fork, so hook-run tests cannot touch the real repository. Proved both ways withGIT_DIRpointed at a scratch repo: without the guard the scratch repo gets a moved HEAD anduser.name = Tower Test; with it, nothing changes.type: ["string","null"]; without this the manifests would degrade toany. Regenerated manifests are byte-identical to the committed ones.flake.nixpnpmDeps hash refreshed; web bundle rebuilt (lockfile is a bundle input).Behavior Changes and Affected Users
@hono/node-server2.x (MCP SDK HTTP transport)GIT_DIRand could write into the repoNo user-facing behavior change; no changeset. [skip changeset]
Coverage:
pnpm audit0 (one ignored low with no fix); typecheck, lint, sherif, vscode typecheck,nix build .#pythinker-codeall exit 0; full suite 18,619 passed, 3 failed: the stale wire manifest (fixed in this PR) and two known load-only timeouts that pass in isolation (148/148).Checklist
/approve).gen-changesetsskill, or this PR needs no changeset.gen-docsskill, or this PR needs no doc update.