From fae51d853dc2679f46669ba981939fa407dee88f Mon Sep 17 00:00:00 2001
From: Kit Langton <kit.langton@gmail.com>
Date: Thu, 2 Jul 2026 20:56:56 -0400
Subject: [PATCH] refactor(core): dedupe context epoch initialization

Share one insertInitial path between initialize and prepare, and
document the runner's ordering constraint: epoch initialization runs
before promotion so a blocked System Context leaves prompts pending,
while reconciliation runs after promotion so ContextUpdated messages
sequence after promoted input.
---
 packages/core/src/session/context-epoch.ts | 19 +++++++++++--------
 packages/core/src/session/runner/llm.ts    |  4 ++++
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/packages/core/src/session/context-epoch.ts b/packages/core/src/session/context-epoch.ts
index 65b17a86a4..227214569b 100644
--- a/packages/core/src/session/context-epoch.ts
+++ b/packages/core/src/session/context-epoch.ts
@@ -8,7 +8,6 @@ import { SystemContext } from "../system-context/index"
 import { ContextSnapshotDecodeError } from "./error"
 import { SessionEvent } from "./event"
 import { SessionHistory } from "./history"
-import { SessionInput } from "./input"
 import { SessionMessage } from "./message"
 import { SessionSchema } from "./schema"
 import { SessionContextEpochTable } from "./sql"
@@ -47,11 +46,7 @@ const prepareOnce = Effect.fnUntraced(function* (
     [context, find(db, sessionID), SessionHistory.latestCompaction(db, sessionID)],
     { concurrency: "unbounded" },
   )
-  if (!stored) {
-    const generation = yield* SystemContext.initialize(value)
-    const baselineSeq = yield* insert(db, sessionID, generation)
-    return { baseline: generation.baseline, baselineSeq }
-  }
+  if (!stored) return yield* insertInitial(db, sessionID, value)
 
   const snapshot = yield* Schema.decodeUnknownEffect(SystemContext.Snapshot)(stored.snapshot).pipe(
     Effect.mapError((error) => new ContextSnapshotDecodeError({ sessionID, details: String(error) })),
@@ -82,8 +77,16 @@ const initializeOnce = Effect.fnUntraced(function* (
   context: Effect.Effect<SystemContext.SystemContext>,
   sessionID: SessionSchema.ID,
 ) {
-  if (yield* exists(db, sessionID)) return
-  const generation = yield* context.pipe(Effect.flatMap(SystemContext.initialize))
+  if (yield* exists(db, sessionID)) return undefined
+  return yield* insertInitial(db, sessionID, yield* context)
+})
+
+const insertInitial = Effect.fnUntraced(function* (
+  db: DatabaseService,
+  sessionID: SessionSchema.ID,
+  value: SystemContext.SystemContext,
+) {
+  const generation = yield* SystemContext.initialize(value)
   const baselineSeq = yield* insert(db, sessionID, generation)
   return { baseline: generation.baseline, baselineSeq }
 })
diff --git a/packages/core/src/session/runner/llm.ts b/packages/core/src/session/runner/llm.ts
index f9f5e37ffb..66760e1cbb 100644
--- a/packages/core/src/session/runner/llm.ts
+++ b/packages/core/src/session/runner/llm.ts
@@ -168,6 +168,10 @@ const layer = Layer.effect(
       if (session.location.directory !== location.directory || session.location.workspaceID !== location.workspaceID)
         return yield* Effect.interrupt
       const agent = yield* agents.select(session.agent)
+      // Epoch initialization runs before promotion so a blocked System Context fails the
+      // turn while prompts are still pending in the durable inbox; a retry re-drains them.
+      // Reconciliation (`prepare` below) runs after promotion so ContextUpdated messages
+      // sequence after the promoted user input.
       const initialized = yield* SessionContextEpoch.initialize(db, loadSystemContext(agent), session.id)
       const toolFibers = yield* FiberSet.make<void, ToolOutputStore.Error>()
       let needsContinuation = false