Harness spec 3.1.0: the prefix stays still, in the CLI

The system prompt is made once per session (start, compaction, model
switch), kept in session_meta and resent byte for byte; it holds no
date. What changes mid-session -- the date, a mode the person chose, a
plan or memory or instruction file they edited, a personality, MCP
instructions that arrived later -- is a <session-note> on the next user
message, stored with it. The tool list is fixed for the session:
plan_submit is always offered and answers unavailable outside plan
mode, the wrap-up keeps the tools and runs no call, a withdrawn tool
stays listed and answers its refusal; the first request waits up to
mcp_wait_ms for MCP servers. Compaction asks for its summary as the
next turn of the same conversation. Cached input tokens are parsed
(incl. llama.cpp timings), stored per request and shown in /context.

Spec: context.md §7/§10, loop.json context.note (+ plan_ended,
plan_own, personal, empty, mcp_wait_ms), modes.json plan.refused,
compact.md without the transcript heading. Conformance area prefix.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

src/session/store.ts

@@ -2,7 +2,8 @@ import { Database } from "bun:sqlite"
 import { mkdirSync } from "node:fs"
 import { join } from "node:path"
 import { paths } from "../config/paths.ts"
-import type { Message } from "../provider/types.ts"
+import type { Message, Usage } from "../provider/types.ts"
+import { isNote } from "./prefix.ts"
 
 // Sessions and their messages, in ~/.local/share/lembas/sessions.db. Message text is also
 // indexed with FTS5 so past sessions can be searched (session_search).
@@ -53,6 +54,11 @@ CREATE TABLE IF NOT EXISTS results (
   json TEXT NOT NULL, text TEXT NOT NULL,
   PRIMARY KEY (session_id, id)
 );
+CREATE TABLE IF NOT EXISTS requests (
+  id INTEGER PRIMARY KEY AUTOINCREMENT, session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  created INTEGER NOT NULL, model TEXT NOT NULL, kind TEXT NOT NULL,
+  input INTEGER NOT NULL, output INTEGER NOT NULL, reasoning INTEGER, cached INTEGER, estimated INTEGER NOT NULL DEFAULT 0
+);
 CREATE TABLE IF NOT EXISTS session_meta (
   session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE, key TEXT NOT NULL, value TEXT NOT NULL,
   PRIMARY KEY (session_id, key)
@@ -70,7 +76,16 @@ export const CWD_META = "cwd"
 
 export function plainText(m: Message): string {
   if (m.role === "tool") return m.content
-  return m.parts.map((p) => (p.type === "text" || p.type === "reasoning" ? p.text : p.type === "tool_call" ? `${p.name} ${p.args}` : "")).join("\n")
+  // A session note is the harness's, not the person's words: not searched.
+  return m.parts.map((p) => (p.type === "text" ? (m.role === "user" && isNote(p.text) ? "" : p.text) : p.type === "reasoning" ? p.text : p.type === "tool_call" ? `${p.name} ${p.args}` : "")).join("\n")
+}
+
+/** One request's usage as the store keeps it (harness context.md §10 rule 6): what it was for — a
+ *  step of a turn, or a compaction's summary — and the cached input tokens where the server said. */
+export interface RequestRow extends Usage {
+  model: string
+  kind: "step" | "compaction"
+  created?: number
 }
 
 export interface Row {
@@ -225,6 +240,19 @@ export class Store {
     }
   }
 
+  /** Record one request's usage. */
+  request(sessionId: string, r: RequestRow) {
+    this.db
+      .query("INSERT INTO requests (session_id, created, model, kind, input, output, reasoning, cached, estimated) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)")
+      .run(sessionId, Date.now(), r.model, r.kind, r.input, r.output, r.reasoning ?? null, r.cached ?? null, r.estimated ? 1 : 0)
+  }
+
+  /** A session's requests, oldest first. */
+  requests(sessionId: string): RequestRow[] {
+    const rows = this.db.query("SELECT created, model, kind, input, output, reasoning, cached, estimated FROM requests WHERE session_id = ? ORDER BY id").all(sessionId) as (Omit<RequestRow, "estimated" | "reasoning" | "cached"> & { estimated: number; reasoning: number | null; cached: number | null })[]
+    return rows.map(({ estimated, reasoning, cached, ...r }) => ({ ...r, ...(reasoning !== null ? { reasoning } : {}), ...(cached !== null ? { cached } : {}), ...(estimated ? { estimated: true } : {}) }))
+  }
+
   /** Something a session keeps besides its messages, as JSON. */
   meta<T>(sessionId: string, key: string): T | undefined {
     const r = this.db.query("SELECT value FROM session_meta WHERE session_id = ? AND key = ?").get(sessionId, key) as { value: string } | null