Epic: Harness Layer Separation — virtual layers via manifest metadata (v3.0.0)

[cheddarfox]

Epic: Harness Layer Separation (v3.0.0)\n\nDeferred from: SAW-1 (Fork-Friendly Harness Update Mechanism)\nBlocked by: v2.10.0 multi-domain sync must be stable and validated\n\n### Description\n\nImplement Proposal C from GH#28: split the harness into composable layers (core methodology / project config / documentation) using manifest metadata — NOT filesystem restructuring. This preserves Claude Code's path auto-discovery while enabling per-layer sync strategies.\n\n### Rationale\n\nPhysical restructuring would break all existing forks. Virtual layers via manifest layer_overrides and sync.layer_strategy provide the same benefits without breaking changes. Deferred to v3.0.0 after manifest system is proven.\n\n### Implementation Notes (from v2.10.0 session)\n\nFoundation now exists: v2.10.0 shipped the multi-domain sync engine with schema v1.1. The sync_scope, root-relative paths, manifest-authoritative model, and domain loop architecture are all in place. Layer separation would extend this by:\n\n1. Layer definitions in manifest — schema v2.0 adds layers section mapping files to layers (core/config/docs)\n2. Per-layer sync strategy — sync.layer_strategy allowing different conflict_strategy per layer (e.g., upstream-wins for core, local-wins for config)\n3. Layer-aware diff — do_diff() groups output by layer, not just by domain\n4. Layer-conditional substitutions — some layers may skip substitution (docs layer keeps placeholders for template users)\n\n### What v2.10.0 already provides that this builds on\n- Multi-domain sync loop (iterate per domain)\n- v1.0/v1.1 manifest version branching (ready for v2.0)\n- Root-relative path model (layer paths would also be root-relative)\n- Manifest-authoritative model (layers would be manifest-declared)\n- Protected/replaced/renames work across domains (would work across layers)\n\n### Open questions for decomposition\n- Should layers be orthogonal to domains (a layer spans multiple domains) or nested (each domain has layers)?\n- How does layer separation interact with sync_scope? Are layers a refinement within a domain or a cross-cutting concern?\n- Should manifest init auto-detect layers from file patterns, or is layer assignment always manual?\n- What's the migration path from v1.1 manifests (no layers) to v2.0 (with layers)?\n\n### Deferred release domains\nv2.10.0 explicitly deferred docs/, scripts/, patterns_library/ from sync_scope. These are the natural candidates for a "docs" or "release" layer in v3.0.0. Layer separation could gate these behind a separate sync strategy (e.g., opt-in, manual review only).\n\n### Estimated scope\nNot yet decomposed. Likely 5-8 stories, ~20-30 points. Requires SA design review before decomposition."