docs(flake): annotate KEEP+DEP rationale (standards#102)

[hyperpolymath]

Refs standards#101 standards#102.

Per the Nix-mirror retirement campaign (Wave 6), file-soup's flake is LOAD-BEARING (KEEP+DEP): the dev shell is the sole source of the full Rust dev env (rust-overlay rustToolchain + rust-src/rustfmt/clippy, pkg-config, just, cargo-watch/audit/outdated/license, openssl, git) plus the full shell's tokei/ripgrep/fd/bat/exa/cargo-flamegraph/cargo-criterion. guix.scm uses cargo-build-system with zero declared inputs.

This PR adds the rule-3 annotation so the flake's retention is self-documenting. No package-set change.

🤖 Generated with Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 27 issues detected

Severity	Count
🔴 Critical	10
🟠 High	14
🟡 Medium	3

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Must be in .machine_readable/ only",
    "type": "banned",
    "file": "META.scm",
    "action": "move",
    "rule_module": "root_hygiene",
    "severity": "critical"
  },
  {
    "reason": "Must be in .machine_readable/ only",
    "type": "banned",
    "file": "STATE.scm",
    "action": "move",
    "rule_module": "root_hygiene",
    "severity": "critical"
  },
  {
    "reason": "Must be in .machine_readable/ only",
    "type": "banned",
    "file": "ECOSYSTEM.scm",
    "action": "move",
    "rule_module": "root_hygiene",
    "severity": "critical"
  },
  {
    "reason": "Required file missing",
    "type": "missing",
    "file": "0-AI-MANIFEST.a2ml",
    "action": "create",
    "rule_module": "root_hygiene",
    "severity": "high"
  },
  {
    "reason": "No test directory or test files found",
    "type": "no_tests",
    "file": "/home/runner/work/file-soup/file-soup",
    "action": "flag",
    "rule_module": "honest_completion",
    "severity": "high",
    "deduction": 20
  },
  {
    "reason": "Issue in quality.yml",
    "type": "missing_workflow",
    "file": "quality.yml",
    "action": "create",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Issue in security-policy.yml",
    "type": "missing_workflow",
    "file": "security-policy.yml",
    "action": "create",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in secret-scanner.yml",
    "type": "missing_workflow",
    "file": "secret-scanner.yml",
    "action": "create",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
    "type": "unpinned_action",
    "file": "governance.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "unwrap() without prior check -- DoS via panic (5 occurrences, CWE-754)",
    "type": "unwrap_without_check",
    "file": "/home/runner/work/file-soup/file-soup/plugins/version-detection/src/lib.rs",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  }
]

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