fix(agent-runner): open inbound.db fresh per messages_in read

Cached singleton can return stale rows on virtiofs/NFS mounts,
causing follow-up messages to silently never be polled. Add
openInboundDb() with mmap_size=0 and switch the three messages_in
readers to it.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

container/agent-runner/src/db/connection.ts

@@ -28,11 +28,37 @@ let _inbound: Database | null = null;
 let _outbound: Database | null = null;
 let _heartbeatPath: string = DEFAULT_HEARTBEAT_PATH;
 
-/** Inbound DB — container opens read-only (host is the sole writer). */
+/**
+ * Avoid all cached db reads; open inbound.db read-only with mmap and page cache disabled. 
+ * 
+ * Use this (not getInboundDb) for readers that need to see host-written rows
+ * promptly — e.g. messages_in polling. Caller must .close() the returned
+ * connection (try/finally).
+ *
+ * Needed for mounts where host writes don't reliably invalidate
+ * SQLite's caches: virtiofs (Colima, Lima, Podman Machine, Apple
+ * Container), NFS. 
+ * 
+ * Cost is microseconds per query, so safe for universal use.
+ */
+export function openInboundDb(): Database {
+  const db = new Database(DEFAULT_INBOUND_PATH, { readonly: true });
+  db.exec('PRAGMA busy_timeout = 5000');
+  db.exec('PRAGMA mmap_size = 0');
+  return db;
+}
+
+/**
+ * Inbound DB — long-lived singleton, OK for tables the host writes once
+ * at spawn and never again (destinations, session_routing). For
+ * messages_in polling — where the host writes continuously and a stale
+ * view causes the pollHandle hang — use `openInboundDb()` instead.
+ */
 export function getInboundDb(): Database {
   if (!_inbound) {
     _inbound = new Database(DEFAULT_INBOUND_PATH, { readonly: true });
     _inbound.exec('PRAGMA busy_timeout = 5000');
+    _inbound.exec('PRAGMA mmap_size = 0');
   }
   return _inbound;
 }

container/agent-runner/src/db/messages-in.ts

@@ -8,7 +8,7 @@
  * processing_ack. The host reads processing_ack to sync message lifecycle.
  */
 import { getConfig } from '../config.js';
-import { getInboundDb, getOutboundDb } from './connection.js';
+import { openInboundDb, getOutboundDb } from './connection.js';
 
 export interface MessageInRow {
   id: string;
@@ -50,31 +50,35 @@ function getMaxMessagesPerPrompt(): number {
  * trigger=1 separately (see src/db/session-db.ts).
  */
 export function getPendingMessages(): MessageInRow[] {
-  const inbound = getInboundDb();
+  const inbound = openInboundDb();
   const outbound = getOutboundDb();
 
-  const pending = inbound
+  try {
-    .prepare(
+    const pending = inbound
-      `SELECT * FROM messages_in
+      .prepare(
-       WHERE status = 'pending'
+        `SELECT * FROM messages_in
-         AND (process_after IS NULL OR datetime(process_after) <= datetime('now'))
+         WHERE status = 'pending'
-       ORDER BY seq DESC
+           AND (process_after IS NULL OR datetime(process_after) <= datetime('now'))
-       LIMIT ?`,
+         ORDER BY seq DESC
-    )
+         LIMIT ?`,
-    .all(getMaxMessagesPerPrompt()) as MessageInRow[];
+      )
+      .all(getMaxMessagesPerPrompt()) as MessageInRow[];
 
-  if (pending.length === 0) return [];
+    if (pending.length === 0) return [];
 
-  // Filter out messages already acknowledged in outbound.db
+    // Filter out messages already acknowledged in outbound.db
-  const ackedIds = new Set(
+    const ackedIds = new Set(
-    (outbound.prepare('SELECT message_id FROM processing_ack').all() as Array<{ message_id: string }>).map(
+      (outbound.prepare('SELECT message_id FROM processing_ack').all() as Array<{ message_id: string }>).map(
-      (r) => r.message_id,
+        (r) => r.message_id,
-    ),
+      ),
-  );
+    );
 
-  // Reverse: we fetched DESC to take the most recent N, but the agent
+    // Reverse: we fetched DESC to take the most recent N, but the agent
-  // should see them in chronological order (oldest first).
+    // should see them in chronological order (oldest first).
-  return pending.filter((m) => !ackedIds.has(m.id)).reverse();
+    return pending.filter((m) => !ackedIds.has(m.id)).reverse();
+  } finally {
+    inbound.close();
+  }
 }
 
 /** Mark messages as processing — writes to processing_ack in outbound.db. */
@@ -112,7 +116,12 @@ export function markFailed(id: string): void {
 
 /** Get a message by ID (read from inbound.db). */
 export function getMessageIn(id: string): MessageInRow | undefined {
-  return getInboundDb().prepare('SELECT * FROM messages_in WHERE id = ?').get(id) as MessageInRow | undefined;
+  const inbound = openInboundDb();
+  try {
+    return inbound.prepare('SELECT * FROM messages_in WHERE id = ?').get(id) as MessageInRow | undefined;
+  } finally {
+    inbound.close();
+  }
 }
 
 /**
@@ -120,19 +129,23 @@ export function getMessageIn(id: string): MessageInRow | undefined {
  * Reads from inbound.db, checks processing_ack to skip already-handled responses.
  */
 export function findQuestionResponse(questionId: string): MessageInRow | undefined {
-  const inbound = getInboundDb();
+  const inbound = openInboundDb();
   const outbound = getOutboundDb();
 
-  const response = inbound
+  try {
-    .prepare("SELECT * FROM messages_in WHERE status = 'pending' AND content LIKE ?")
+    const response = inbound
-    .get(`%"questionId":"${questionId}"%`) as MessageInRow | undefined;
+      .prepare("SELECT * FROM messages_in WHERE status = 'pending' AND content LIKE ?")
+      .get(`%"questionId":"${questionId}"%`) as MessageInRow | undefined;
 
-  if (!response) return undefined;
+    if (!response) return undefined;
 
-  // Check it hasn't been acked already
+    // Check it hasn't been acked already
-  const acked = outbound.prepare('SELECT 1 FROM processing_ack WHERE message_id = ?').get(response.id);
+    const acked = outbound.prepare('SELECT 1 FROM processing_ack WHERE message_id = ?').get(response.id);
-  if (acked) return undefined;
+    if (acked) return undefined;
 
-  return response;
+    return response;
+  } finally {
+    inbound.close();
+  }
 }