chore: refresh stale CI notes + sync drifted Deno fixtures

[hyperpolymath]

Optional housekeeping from the #138 / standalone-CI thread. Docs + regenerated test fixtures only — no source change.

1. .claude/CLAUDE.md — refresh the stale "known-failing baseline checks"

Now that CI is standalone + green on main (#604), several entries were out of date:

• vscode-smoke → now passes (self-contained; skips cleanly without the optional npm package).
• migration-assistant → passes on current main (only red on pre-ci(migration-assistant): fix smoke-parse for tree-sitter-cli 0.25 #342 bases).
• governance → replaced by the self-contained local gate (tools/ci/governance-standalone.sh); the old estate Language / package anti-pattern policy sub-check no longer runs.
• Hypatia comment counts refreshed (~43–71); clarified it's a delta in your changed files that matters, and the Hypatia check gates separately (green).
• Recorded the two startup_failure classes that bit the repo for days so they aren't reintroduced: (1) the Actions "allowed actions" policy rejects tag-pinned refs at run-creation → pin every uses: to a full SHA; (2) BP008 reusable-caller concurrency: stacking.

2. tests/codegen-deno/*.deno.js — sync 3 drifted snapshots

3 of 30 committed Deno-ESM snapshots had drifted from current codegen output (runtime-preamble evolution — WASI fd_write import, pixi/ipc bindings); regenerated. All deno harnesses still pass under node.

Verified

dune test green · tools/run_codegen_deno_tests.sh all harnesses pass.

🤖 Generated with Claude Code

https://claude.ai/code/session_01Lz7pRcec2Z3tVtaAhvB3M8

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Generated by Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 43 issues detected

Severity	Count
🔴 Critical	2
🟠 High	25
🟡 Medium	16

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Action denoland/setup-deno@v2 needs attention",
    "type": "unpinned_action",
    "file": "publish-jsr.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in scorecard-enforcer.yml",
    "type": "scorecard_publish_with_run_step",
    "file": "scorecard-enforcer.yml",
    "action": "split_scorecard_publish_job",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Issue in instant-sync.yml",
    "type": "secret_action_without_presence_gate",
    "file": "instant-sync.yml",
    "action": "peter-evans/repository-dispatch",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Shell execution -- validate input before passing to shell (1 occurrences, CWE-78)",
    "type": "js_exec_sync",
    "file": "/home/runner/work/affinescript/affinescript/packages/affinescript-cli/mod.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  },
  {
    "reason": "Shell execution -- validate input before passing to shell (2 occurrences, CWE-78)",
    "type": "js_exec_sync",
    "file": "/home/runner/work/affinescript/affinescript/packages/affine-vscode/mod.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  },
  {
    "reason": "Shell execution -- validate input before passing to shell (1 occurrences, CWE-78)",
    "type": "js_exec_sync",
    "file": "/home/runner/work/affinescript/affinescript/affinescript-vite/src/affine-plugin-improved.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  },
  {
    "reason": "expect() in hot path (32 occurrences, CWE-754)",
    "type": "expect_in_hot_path",
    "file": "/home/runner/work/affinescript/affinescript/affinescriptiser/src/codegen/wasm_gen.rs",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "medium"
  },
  {
    "reason": "expect() in hot path (29 occurrences, CWE-754)",
    "type": "expect_in_hot_path",
    "file": "/home/runner/work/affinescript/affinescript/affinescriptiser/src/codegen/affine_gen.rs",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "medium"
  },
  {
    "reason": "unsafe block -- requires SAFETY comment (2 occurrences, CWE-676)",
    "type": "unsafe_block",
    "file": "/home/runner/work/affinescript/affinescript/runtime/src/panic.rs",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "medium"
  },
  {
    "reason": "unsafe block -- requires SAFETY comment (1 occurrences, CWE-676)",
    "type": "unsafe_block",
    "file": "/home/runner/work/affinescript/affinescript/runtime/src/alloc.rs",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "medium"
  }
]

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