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mode, the wrap-up keeps the tools and runs no call, a withdrawn tool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>

tests/library.test.ts

@@ -155,10 +155,11 @@ test("the tools: knowledge_search is offered only with something to search; a pr
   lib.putDocument("private", { title: "Diary", source: "d", text: "The pump primes in my dreams." })
   await app.engine.prompt("anything")
   expect(offered()).not.toContain("knowledge_search")
-  // A document in the project's base: offered, and only that base is searched.
+  // A document in the project's base: offered from the next session — the tool list is the
+  // session's, decided as it starts (harness context.md §10) — and only that base is searched.
   const pump = lib.putDocument("manuals", { title: "Pump", source: "p", text: "The pump primes in thirty seconds." })
   fake.requests.length = 0
-  app.engine.messages = []
+  app.newSession()
   await app.engine.prompt("how long does the pump take to prime?")
   expect(offered()).toContain("knowledge_search")
   const results = app.engine.messages.filter((m) => m.role === "tool").map((m) => (m.role === "tool" ? m.content : ""))