fix: report the real cause when check-env.cjs's npm-version check fails
Discovered blocking this PR's own Windows CI (unrelated to this PR's actual diff, fixed inline per this repo's no-defer policy): PR #4552's "full test (windows-latest, 24, shard 2/3)" job failed tests/check-env.test.cjs's npm-version subtest with "npm binary not found on PATH" under chunk 5/9's heavy load (51 concurrent files, 5+ minutes). Root-caused via the CI log: the check's spawnSync call used a 10s timeout, and every failure mode -- ENOENT, a signal-killed timeout, a non-zero exit, a thrown spawn error -- collapsed into that one message (only `res.status === 0 && res.stdout` was checked), so a genuine npm.cmd cold-start timeout under contention was indistinguishable from npm actually being absent. Extracted the reason-selection into describeNpmVersionCheckFailure, a pure function in the new scripts/lib/npm-version-check-diagnosis.cjs (kept out of check-env.cjs itself, which runs its CLI unconditionally on require with no `require.main === module` guard, so the pure logic can be unit-tested without triggering a real environment check). Reports ENOENT, signal-kill, non-zero-exit, and thrown-error cases distinctly. Does NOT raise the 10s timeout itself -- a slow subprocess under contention is a cost to reduce, not a tolerance to widen. Also fixed a stale tsconfig.build.tsbuildinfo incremental-build cache discovered while verifying this change: npm run build:lib was silently omitting gsd-core/bin/lib/markdown-table.cjs (a real, needed compiled module -- src/state-document.cts requires it), which only surfaced via npm run lint:generated-sync's gen-health-docs check failing with Cannot find module. Deleting the cache and rebuilding fresh restored it; docs/INVENTORY-MANIFEST.json needed no net change once the build was genuinely complete. Manually verified describeNpmVersionCheckFailure's five branches directly (ENOENT, signal-kill, non-zero exit, thrown error, defensive default) before wiring the test file, since this repo blocks local node --test. Re-ran node scripts/check-env.cjs directly to confirm the real success path is unaffected. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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type: Security
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pr: 0
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pr: 4552
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**Pinned the transitive `hono` dependency to `>=4.13.5`** — fixes a moderate-severity path-traversal/DoS advisory chain (GHSA-gqvv-2mrq-wpjv, GHSA-g6gw-c38x-mqfc, GHSA-crvj-82cr-hjcx) in `hono <4.13.5`, pulled in transitively via `@anthropic-ai/claude-agent-sdk` -> `@modelcontextprotocol/sdk`. Discovered blocking `tests/npm-integrity-gate.test.cjs` while verifying #4460; fixed inline per this repo's no-defer policy rather than left for a separate PR. (#4460)
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type: Fixed
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pr: 4552
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**`npm run check:env`'s npm-version check no longer misreports a timeout as a missing binary** — every `spawnSync` failure mode (ENOENT, a signal-killed timeout under load, a non-zero exit, a thrown spawn error) used to collapse into one message, "npm binary not found on PATH." Discovered live: an unrelated PR's Windows CI shard failed this check under heavy concurrent test load, and the message made a real timeout indistinguishable from npm genuinely being absent. The reason is now reported accurately; the check's own 10s timeout is unchanged. (#4460)
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