digest-aware serialized extraction + chain simplification replace the spine stage

Owner live-test verdict on the spine (2026-09-30): no perceptible gain —
the real problems (restatement nodes, shallow re-derivations, same
conclusion from many angles) are mint-time issues a post-hoc chain
minter cannot fix. This arc moves assembly INTO the extractor and adds
the deterministic dedupe the owner specified:

- Digest-aware extraction: each stretch's extractor prompt carries THE
  GRAPH SO FAR (its own source's merged propositions + chains, ids
  verbatim); build on existing ids instead of restating, lean on
  established conclusions as premises. Mixed-namespace chain endpoints
  (fresh p-ids OR existing n_-ids) validated at the submit seam.
- Serialized per source: a source's batches/chunks run strictly in
  order (each extract reads every earlier merge); cross-source runs
  stay parallel; source-wide abort stops the loop. The spine stage,
  role, phase, usage stage, cost row, and setup roster are gone.
- Core-ideas prompt: goal reframed as uncovering core ideas and showing
  how everything derives from the foundations; direction upward, prefer
  lean derivations, never re-derive what the graph already holds.
- Chain simplification (merger maintenance): simplifyChains drops
  provably redundant chains at every merge — prefer-fewest-premises +
  ancestry-cover ([A,B]⟹X with [X,C]⟹Y covers [A,B,C]⟹Y, transitive);
  same-key provenance lines drop together; rewriteLedgers under the
  audit lock; droppedChains counted separately in stats.

Chunk budget stays 8192 (owner: keep for now, maybe lower later).

src/agent/subagents/submit-agent.ts

@@ -16,8 +16,8 @@ import type { PiEngine } from "../models.ts";
 import { runSubagent } from "./pi-run.ts";
 
 // ── the weak-model string-heal (owner, 2026-09-28; moved here from
-// extraction.ts with the spine stage, 2026-09-30 — the heal is wire-format
-// medicine shared by every submit agent) ──
+// extraction.ts with the digest-aware redesign, 2026-09-30 — the heal
+// is wire-format medicine shared by every submit agent) ──
 //
 // OpenRouter log evidence: weak models under a big submit payload often
 // emit a whole array as ONE JSON-STRING instead of a native array