chore: fill template placeholders with project identity (Part A)

[hyperpolymath]

Why

Part A of the in-repo hygiene work (you chose "2 then 1"). The repo shipped with unfilled RSR template {{TOKEN}} placeholders across ~55 functional files; this fills them with the real project identity so the repo reads as a real project, not a template.

What

Controlled substitution over every {{...}} file except intentional templates, mapping tokens to:
hyperpolymath / gv-clade-index / Jonathan D.A. Jewell / j.d.a.jewell@open.ac.uk / MPL-2.0 / 2026 / clade-registry-api / 8080 / ghcr.io/hyperpolymath / hyperpolymath.github.io, plus derived descriptions (purpose, lang-stack, build/test cmds, invariants).

Deliberately left untouched (placeholders are intentional):

• .machine_readable/svc/k9/template-*.k9.ncl, svc/k9/examples/*, docs/decisions/0000-template.adoc, .machine_readable/ai/PLACEHOLDERS.adoc, examples/web-project-deno.json
• token-documentation files: PROOF-NEEDS.md, container/README.adoc, container/0.1-AI-MANIFEST.a2ml, the methodology.a2ml reject-if-contains rule, and the Justfile init recipe
• Just's own {{lowercase}} interpolations (only the {{OWNER}} template defaults were filled)

Surgical fixes:

• .github/SECURITY.md + CODE_OF_CONDUCT.md: removed the "delete before publishing" instruction blocks; dropped PGP key/fingerprint references (no PGP key offered — GitHub Security Advisories is the primary channel)
• .github/.mailmap: dropped the empty alternate-email slot

Verified

• No residual {{...}} outside the intentional set.
• Changed TOML/YAML/CFF/JSON parse cleanly (container/compose.toml uses a pre-existing selur-compose multi-line-inline-table dialect — unchanged here, fails strict tomllib on main too).
• Justfile diff confirmed safe (Just interpolations intact); worker tests 37/37 still pass.

Part B (workflow-hardening) follows as a separate PR.

🤖 Generated with Claude Code

https://claude.ai/code/session_01UCnxjXkN6uDj9YSANuGEgR

---

Generated by Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 39 issues detected

Severity	Count
🔴 Critical	1
🟠 High	7
🟡 Medium	31

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Issue in release.yml",
    "type": "missing_timeout_minutes",
    "file": "release.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in release.yml",
    "type": "missing_timeout_minutes",
    "file": "release.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in release.yml",
    "type": "missing_timeout_minutes",
    "file": "release.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in rhodibot.yml",
    "type": "missing_timeout_minutes",
    "file": "rhodibot.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in static-analysis-gate.yml",
    "type": "missing_timeout_minutes",
    "file": "static-analysis-gate.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in static-analysis-gate.yml",
    "type": "missing_timeout_minutes",
    "file": "static-analysis-gate.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "reason": "Issue in static-analysis-gate.yml",
    "type": "missing_timeout_minutes",
    "file": "static-analysis-gate.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  },
  {
    "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": "Issue in scorecard.yml",
    "type": "scorecard_wrapper_missing_job_permissions",
    "file": "scorecard.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Issue in codeql.yml",
    "type": "codeql_missing_actions_language",
    "file": "codeql.yml",
    "action": "flag",
    "rule_module": "workflow_audit",
    "severity": "medium"
  }
]

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