docs(architecture): scaffold animated Protocol Reference section

[chefsale]

What

Starts a new Protocol Reference under architecture/protocol/ — an implementation-level guide aimed at someone building an independent Calimero node from scratch. It's organised around the life of one operation (birth → convergence) rather than crate by crate.

This is a walking skeleton / template-setter, not the full reference. It establishes the structure, voice, and diagram style so the remaining chapters can be filled in consistently.

Contents

• protocol/index.html — section landing page: the one core idea, an animated life-of-an-operation sequence diagram, the four writing principles, and the 10-chapter TOC with draft/planned status chips.
• protocol/concepts.html — Chapter 1 (Concepts & Scopes): defines the scope abstraction (the replication/encryption/membership/convergence domain) with an animated scope-tree diagram.
• seq-diagram.js + styles.css — the step-cascade animated-SVG engine, extracted out of sequence-diagrams.html into shared assets so every page reuses it. Data-driven sequence diagrams + a prefers-reduced-motion fallback.
• nav.js — registers the new section and tidies two auto-generated PR-title nav labels into clean names.

How to preview

⚠️ GitHub Pages here only deploys from master (pages.yml), so this PR has no auto preview URL. To view locally:

cd architecture && python3 -m http.server 8000
# open http://localhost:8000/protocol/

Notes / follow-ups

• All diagrams are animated SVG (no mermaid), matching the existing docs style.
• Before merging to master, we should fence architecture/protocol/** out of the doc auto-update bot so hand-authored pages aren't clobbered.
• Next chapters to author: 3 (Operations & the DAG) + 4 (Projection & root hash).

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