docs: calibrate specs/ to codebase truth (31 files, index restructure)

[auto-wood]

Summary

Docs-maintenance round 2026-09-29-specs-truth-maintenance: 16 read-only audit seats verified all 65 spec files against the codebase (code = ground truth); 24 drift files fixed across 9 commits by serial single-writer architect waves; specs/README.md + root AGENTS.md indexes restructured.

Key corrections

• Retired topologies explicitly historicized: local-cloud-crate-architecture → historical crate-graph record; local-runtime-boundary daemon host sections historical; current owners = apps/nexus-service (serves /v1/daemon/*), Electron desktop, nexus-runtime Connect host
• creator-run-preset-entry → retired runner record (v1.193 P2-T1, no replacement preset dispatch); creator-workflow auto-chain/resume-chain retired
• entity-scope-model BlockType enum synced to the 19-value wire enum (incl. era); dead nexus-kb anchors → nexus-knowledge
• ACP SDK pin 2.1.0 → =2.2.0; capability roster recounted (30 static IDs = 28 nexus.* + 2 fs/*); capability-registry Master/Draft ambiguity resolved
• llm-extract: production preset routing marked unshipped (review-time pathway only); preset-conditional-routing → shipped normative SSOT framing
• novel-writing/sync-contract: shipped-library status with real owner (crates/nexus-orchestration/src/sync_module.rs); StoryBundle cloud transport explicitly unwired; V1.36 historical contract preserved
• specs/README.md two-way index/disk diff empty (62/62); 108 links resolve; root AGENTS.md +7 subdirectory rows; 4 missing Document class declarations added

Verification

• Single-seat QC: initial Reject (1 Warning: historical sync-contract content rewritten) → targeted fix 84e00ae76 → re-review Approve, findings [] (.mstar/sdd/2026-09-29-specs-truth-maintenance/review/qc-consolidated.md)
• PM acceptance recorded (docs-only tier, no runtime diff); per-wave before/after evidence with re-verified code anchors
• Code residual registered (not fixed here): R-DOCS-001 — concurrency.md §6.2 successful-acquire stale-holder detection missing in crates/nexus-local-db/src/file_lock.rs::try_acquire (medium, open)

Non-goals

No code/schema/CLI changes; no directory sharding of specs/ (flat layout is canon).

[greptile-apps]

Confidence Score: 5/5

[Low risk] Documentation restructure and cross-reference updates.

The latest change appears safe to merge, though two documentation findings from the previous review remain open.

Findings

1.  Conflicting refresh registration guidance ▶
2.  Stale authoritative design reference ▶

Fix with agent prompt

### Issue 1
.mstar/specs/runtime/reference-knowledge.md:185-187
This new integration note correctly says `nexus.reference.refresh` is registered in the core tool table, but §5 still says it is not registered in `host_tool_registry()` or exposed as a host tool. The core registry registers it as a writable host tool. Readers therefore get conflicting guidance about whether they can dispatch the capability. Please reconcile §5 with the registration, while keeping the separate point that the periodic scheduler is not started.

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

### Issue 2
.mstar/specs/orchestration/orchestration-engine.md:undefined-5
Moving this spec into `specs/orchestration/` leaves the `nexus-orchestration` crate’s “Authoritative design” comment pointing to the removed flat path. Contributors following it cannot reach the current spec. Please update that reference and the other source comments that still cite moved spec paths.

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For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

Summary

The PR reconciles specs with current code ownership and reorganizes them into domain directories. Since the previous review, the only change corrects an external-consumer spec link in docs/ARCHITECTURE.md.

_{Reviews (4) · Last reviewed commit: "docs: fix stale knowledge-path link to s..."}