[codex] Consolidate specs under spec directory

[sungjunlee]

Summary

• Move the canonical charter artifact to spec/charter.md with root CHARTER.md retained only as a legacy fallback.
• Add spec/README.md, dogfood spec/system-map.md, and a new spec-system-map skill/template.
• Wire charter path resolution through objectives checks, spec-grill signal extraction, backlog-triage alignment guidance, and active docs.

Validation

• node --test over all non-integration JS tests: 409 passed
• node skills/spec-charter/scripts/check-size.js --path spec/charter.md --json
• node skills/dev-backlog/scripts/objectives-check.js --json
• node skills/dev-backlog/scripts/capabilities-doctor.js --json
• node skills/dev-backlog/scripts/component-lint.js --json
• node skills/spec-grill/scripts/extract-signals.js --repo-root . --json
• git diff --check

Closes #161
Closes #162
Closes #163
Closes #164
Closes #165

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: b7137452-18f4-4972-b36d-fd7a94838675

📥 Commits

Reviewing files that changed from the base of the PR and between 19401fc and 36d8419.

📒 Files selected for processing (30)

• AGENTS.md
• CHANGELOG.md
• CLAUDE.md
• README.md
• docs/spec-system-design.md
• skills/backlog-triage/SKILL.md
• skills/dev-backlog/SKILL.md
• skills/dev-backlog/references/process.md
• skills/dev-backlog/scripts/objectives-check.js
• skills/dev-backlog/scripts/objectives-check.test.js
• skills/dev-backlog/scripts/spec-paths.js
• skills/spec-charter/SKILL.md
• skills/spec-charter/references/alignment.md
• skills/spec-charter/references/amendment.md
• skills/spec-charter/references/create.md
• skills/spec-charter/references/objectives.md
• skills/spec-charter/references/reassess.md
• skills/spec-charter/scripts/check-size.js
• skills/spec-charter/scripts/check-size.test.js
• skills/spec-grill/SKILL.md
• skills/spec-grill/references/capabilities.md
• skills/spec-grill/scripts/extract-signals.js
• skills/spec-grill/scripts/extract-signals.test.js
• skills/spec-grill/templates/capabilities.md
• skills/spec-system-map/SKILL.md
• skills/spec-system-map/templates/system-map.md
• spec/README.md
• spec/capabilities.md
• spec/charter.md
• spec/system-map.md

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/spec-layout

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