docs: Update docs to reflect molecule-first paradigm (gt-nam3)

- Add molecule-first paradigm note at top of architecture.md
- Update all spawn examples to include --molecule flag
- Add "Config vs Molecule" section with cognition principle
- Add policy-to-molecule escalation note in federation-design.md
- Update role templates (mayor, witness) with molecule usage

Key message: Gas Town spawns workers on molecules, not just issues.
The issue is seed data; the molecule defines the workflow.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/bootstrap.md

@@ -221,4 +221,4 @@ echo "Bootstrap complete!"
 After bootstrapping:
 1. Start a Mayor session: `gt mayor attach`
 2. Check for work: `bd ready`
-3. Spawn workers as needed: `gt spawn --issue <id>`
+3. Spawn workers with molecules: `gt spawn --issue <id> --molecule mol-engineer-in-box`