fix(validate-a2ml): treat whole .machine_readable/ tree as structural-identity

[hyperpolymath]

Problem

The identity check exempted only .machine_readable/6a2/ typed manifests (structural identity = owning repo + path + filename, no in-file name/agent-id). That rationale applies to the entire .machine_readable/ tree.

rsr-template-repo — the canonical source every RSR repo is built from — itself ships CLADE.a2ml, ANCHOR.a2ml, STATE/ECOSYSTEM, agent_instructions/{debt,coverage,methodology}, ai/AI, policies/*, integrations/* without an in-file identity key. The old check therefore produced estate-wide false positives on every consumer.

Surfaced via idaptik#77: Dogfood Gate reported 15 A2ML errors — 10 were already-fixed false positives (stale pinned SHA), the remaining 5 were exactly these canonical .machine_readable/ docs.

Fix

Generalise the existing 6a2/ exemption to the whole .machine_readable/ tree. Purely subtractive — adds an exemption, cannot introduce new errors.

Verification

• idaptik: 5 → 0 errors (exit 0).
• rsr-template-repo: still flags its 3 non-tree docs (.machine_readable/-external) — exemption is correctly narrow.
• a2ml-validate-action self-dogfood: still flags its pre-existing docs/governance/* (unrelated, not introduced here).
• bash -n clean.

🤖 Generated with Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 8 issues detected

Severity	Count
🔴 Critical	1
🟠 High	1
🟡 Medium	6

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Action actions/upload-artifact@v4 needs attention",
    "type": "unpinned_action",
    "file": "release.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Action actions/download-artifact@v4 needs attention",
    "type": "unpinned_action",
    "file": "release.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "codeql.yml lists `language: javascript-typescript` but the repo has no source files in any CodeQL-scannable language. The analyze job will exit 'no source files' on every run. Switch the matrix to `actions` (which scans workflow files — every repo has those).",
    "type": "codeql_language_matrix_mismatch",
    "file": "codeql.yml",
    "action": "switch_codeql_matrix_to_actions",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "line": 24,
    "reason": "Secret found: Generic API key",
    "type": "secret_detected",
    "file": "/home/runner/work/a2ml-validate-action/a2ml-validate-action/.envrc",
    "action": "revoke_rotate_and_purge",
    "rule_module": "security_errors",
    "severity": "critical"
  },
  {
    "reason": "Nominal-only SAST in a2ml-validate-action: codeql.yml language matrix contains no language present in the repo and lacks `actions`, so CodeQL records zero results on every commit. Remediation: set the CodeQL matrix to `language: actions`.",
    "type": "StaticAnalysis",
    "file": "/home/runner/work/a2ml-validate-action/a2ml-validate-action",
    "action": "auto_fix",
    "rule_module": "scorecard",
    "severity": "medium",
    "remediation": "Add CodeQL or equivalent SAST workflow.",
    "scorecard_check": "SAST"
  },
  {
    "reason": "1 workflow(s) with tag-pinned (not SHA-pinned) actions in a2ml-validate-action",
    "type": "DependencyPinning",
    "file": "/home/runner/work/a2ml-validate-action/a2ml-validate-action",
    "action": "auto_fix",
    "rule_module": "scorecard",
    "severity": "medium",
    "remediation": "Pin GitHub Actions and Docker base images by SHA hash.",
    "scorecard_check": "Pinned-Dependencies"
  },
  {
    "reason": "Repository has 2 non-main remote branch(es). Policy: single main branch only.",
    "type": "GS007",
    "file": ".",
    "action": "delete_remote_branches",
    "rule_module": "git_state",
    "severity": "medium"
  },
  {
    "reason": "Source file missing SPDX-License-Identifier header",
    "type": "SD009",
    "file": "src/interface/ffi/src/main.zig",
    "action": "add_spdx_header",
    "rule_module": "structural_drift",
    "severity": "medium"
  }
]

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