ci: fix standalone-CI fallout — SHA-pin actions, de-trip secret scanner

[hyperpolymath]

Follow-up to #603 (merged). #603 went in via admin bypass with red CI, so main is currently not green — this PR fixes that and completes "ensure standalone CI makes it through CI/CD."

What was still wrong after #603

1. startup_failure persisted on CI / Governance / Secret Scanner — even though Governance/Secret-Scanner became trivial (checkout + run:). Identical failure across totally different file content ⇒ not the content. The one structural difference vs the passing simple workflows (stdlib-naming, workflow-linter, scorecard-enforcer): they pin actions/checkout@<SHA>; ci: make CI standalone (drop estate reusable workflows + third-party setup action) #603 used @v4 tags. The repo's "allowed actions" policy appears to reject tag refs at run-creation.
2. Hypatia check FAILED — "Private Key" detected in tools/ci/secret-scan-standalone.sh: the scanner's literal PEM markers tripped the code-scanner against itself.
3. Hypatia unpinned_action findings (+15) — the @v4 tags violate the repo's SHA-pinning policy (workflow_audit).

Fix

• Re-pin all first-party actions/* to SHAs (revert @v4 → the repo's existing SHAs; only the fictional version comments v6.0.3/v7.0.1 were corrected to v4). This clears the unpinned_action findings and is the fix for the tag-ref startup_failure (SHA-only policy).
• De-trip the secret scanner: the PEM marker is now assembled from fragments, so no full marker literal appears in the file (clears the failing Hypatia "Private Key" alert).
• Fix a latent scanner bug: patterns starting with - need grep -e, else grep parsed them as options and silently matched nothing. Verified: planted PEM and AWS keys are now detected; the tree stays clean.

Verified locally

tools/ci/secret-scan-standalone.sh            → PASS (clean tree)
planted -----BEGIN RSA PRIVATE KEY----- file  → FAIL (detected) ✅
planted AKIA… file                            → FAIL (detected) ✅
no literal 'BEGIN' marker remains in the script
all 4 workflows: valid YAML; zero `actions/*@vN` tag pins (all SHA)

Honest caveat

The SHA-only-policy theory is evidence-based but I can't observe GitHub's run-creation from here. This PR's own CI run is the test: if CI/Governance/Secret Scanner now start (and build/lint/test run), the theory holds. If startup_failure persists despite SHA pins, the remaining cause is an owner-side Settings → Actions → Allowed actions policy I can't change — I'll report that.

Unchanged from #603 and still intentional: hypatia-scan / spark-theatre-gate (estate-proprietary, passing), mirror (cross-forge), release.yml (cross-platform macOS matrix needs ocaml/setup-ocaml).

🤖 Generated with Claude Code

https://claude.ai/code/session_01Lz7pRcec2Z3tVtaAhvB3M8

---

Generated by Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 71 issues detected

Severity	Count
🔴 Critical	2
🟠 High	26
🟡 Medium	43

⚠️ 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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[github-actions]

🔍 Hypatia Security Scan

Findings: 71 issues detected

Severity	Count
🔴 Critical	2
🟠 High	26
🟡 Medium	43

⚠️ 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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