feat: add cognitive substrate pre-action gate

[CodeWithJuber]

Summary

• Adds forge substrate "<task>" [--json] as the single cognitive-substrate pre-action surface.
• Adds forge impact <symbol|file> plus upgraded atlas graph nodes/edges/hashes/reverse impact traversal.
• Ports router/gate rubrics into ForgeKit preflight/route, and exposes MCP tools substrate_check, predict_impact, and assumption_gate while keeping existing tools compatible.
• Adds machine-readable source/substrate.json, Codex/Claude plugin packaging, MCP config, and a cognitive-substrate skill with paper-derived reference map.
• Preserves original Python prototypes under research/python-prototypes/ for evidence/auditability.

Validation

• npm test — 147 passing
• npm run typecheck
• npm run lint — non-failing Biome schema/style infos only
• npm pack --dry-run --json
• Codex plugin validation: validate_plugin.py .
• Skill validation: quick_validate.py global/tools/cognitive-substrate and quick_validate.py skills/cognitive-substrate
• Smoke: forge init, forge doctor, forge substrate "fix auth bug" --json in a temp git repo

Staging

• Same ForgeKit-native implementation pushed to CodeWithJuber/cognitive-substrate-production@95e6630 on main.