feat: two-layer state backend (git-notes + orphan combined) #1013

The Two-Layer Architecture (from blog)

PR #1004 implements git-notes and orphan as separate backends. But the blog post describes them working together as a two-layer architecture:

Layer 1: Git Notes (commit-scoped "why" annotations)
  - Per-agent namespaces: refs/notes/squad/{agent}
  - Thin JSON attached to specific commits
  - Invisible in PR diffs
  - Agents write here during sessions

Layer 2: Orphan Branch (permanent state store)  
  - decisions.md, agent histories, logs
  - The "team diary" — full state
  - Ralph promotes important notes here after PR merge

Ralph bridges the layers:
  - After PR merges, scans notes with promote_to_permanent: true
  - Promotes to decisions.md on orphan branch
  - Notes on rejected PRs are silently ignored (desired behavior)

Why this matters

The blog describes 3 scenarios that break naive solutions:

1. Rejected feature — decision on a rejected PR should NOT be promoted
2. Universal truth — routing change on a rejected PR SHOULD survive
3. Valuable failure — research worth keeping even when feature is rejected

The two-layer architecture handles all three via promote_to_permanent and archive_on_close flags on notes. Single-backend approaches can't distinguish these cases.

What to implement

• Add stateBackend: "two-layer" option in config.json
• When two-layer: agents write commit-scoped notes (layer 1) AND Scribe commits bulk state to orphan (layer 2)
• Ralph promotion: after PR merge, scan notes with promote_to_permanent: true, append to orphan branch decisions.md
• Ralph archival: after PR close (rejected), scan notes with archive_on_close: true, archive to orphan branch
• Notes on rejected PRs without flags: silently ignored (correct behavior)

Reference

• Blog: https://www.tamirdresher.com/blog/2026/03/23/scaling-ai-part7b-git-notes
• Reference repos: tamirdresher/squad-git-notes-reference, tamirdresher/squad-git-notes-demo
• PR feat: wire state backends into all squad operations (worktree, git-notes, orphan, two-layer) #1004 provides the building blocks (both backends work independently)