Stop welding "delivered" onto "read"

The inbox projection used to call `markAgentInboxDelivered` after
appending each message to the agent's session shadow. That helper
sets `agent_messages.read_at = now()` for direct messages and
inserts into `agent_message_reads` for channel messages — the SAME
flags `listAgentInboxUnread` and the public `?unreadOnly=true` API
use to define "unread". So the moment we put a message into the
recipient's transcript, the recipient's own API call returned
nothing pending. The IC prompt told the agent to "respond to ALL
unread messages"; the API said zero unread; the agent posted a
status comment instead of replying. Every silent-employee report
traces back here.

Replay safety lives entirely on `agent_message_projections`
(installed in v46) — that ledger is keyed by `(message_id,
session_id)` and `claimProjection` already short-circuits a re-run
without touching `read_at` at all. The two concepts are now
properly separated:

  - "delivered" (we put it in front of the agent) — tracked by
    the projection ledger, owned by the runtime bridge;
  - "read" (the agent acknowledged it) — tracked by `read_at` and
    `agent_message_reads`, only flipped by the explicit POST
    /messages/{id}/read endpoint the agent calls itself.

`markAgentInboxDelivered` is removed because there is no remaining
caller and its semantics were the bug — keeping it around would
just invite the same mistake again.

src/main/agent-runtime/runtime-bridge.ts

@@ -529,16 +529,17 @@ export class RuntimeBridge {
     // before loading priorMessages — the recipient must observe them
     // as plain user turns in its context.
     //
-    // The projection closure is now atomic: the ledger claim, the
-    // session-shadow append, the thread-event write, and the
-    // delivered-mark all commit inside one `BEGIN IMMEDIATE`
-    // transaction. Pre-v46 layout let those four writes drift apart,
-    // so a crash before the delivered-mark replayed the same inbox
-    // row on the next run and double-populated the transcript. The
-    // `agent_message_projections` ledger is the idempotent gate —
-    // `claimProjection` returns false when the `(message_id,
-    // session_id)` pair is already recorded, so a replay skips the
-    // whole closure.
+    // Replay safety lives entirely on the `agent_message_projections`
+    // ledger. We deliberately do NOT touch `agent_messages.read_at`
+    // here even though that column exists: "we put the message into
+    // the agent's transcript" and "the agent has acknowledged the
+    // message" are two different facts, and welding them onto one
+    // column made every projected message immediately invisible to
+    // the agent's `?unreadOnly=true` API call. The agent then read
+    // its IC prompt ("respond to ALL unread messages"), called the
+    // API, got an empty list, and posted a status comment instead of
+    // replying. The explicit POST /messages/{id}/read is now the
+    // sole signal that flips `read_at`.
     const store = this.getOrCreateStore(payload.taskSessionId);
     const inboxRecords = this.deps.db.listAgentInboxUnread(payload.companyId, payload.agentId);
     if (inboxRecords.length > 0) {
@@ -562,10 +563,6 @@ export class RuntimeBridge {
             record,
           );
         }
-        this.deps.db.markAgentInboxDelivered(
-          payload.agentId,
-          inboxRecords.map((r) => r.id),
-        );
       });
     }
 

src/main/agent-runtime/runtime-message-injector.ts

@@ -128,11 +128,16 @@ export class RuntimeMessageInjector {
   }
 
   /**
-   * Routed from `worker-message-handler` on every `steer-ack`. Commits
-   * the inbox `delivered_at` write when the worker confirms the steer
-   * reached the live Agent; otherwise keeps the row unread and asks
-   * orchestration to wake the recipient so the next `prepareRun` picks
-   * the message up through the regular inbox projection.
+   * Routed from `worker-message-handler` on every `steer-ack`. Confirms
+   * the message reached the live Agent (the bridge already registered
+   * the inbound correlation when it built the projection). On rejection
+   * the recipient is woken so the next `prepareRun` picks the message
+   * up through the regular inbox projection.
+   *
+   * `read_at` is intentionally NOT touched here: "the worker queued
+   * this message onto the agent" is not "the agent replied". The
+   * agent flips `read_at` itself by POSTing /messages/{id}/read once
+   * it has actually processed the row.
    */
   handleSteerAck(correlationId: string, accepted: boolean): void {
     this.resolvePending(correlationId, accepted, "worker_ack");
@@ -148,16 +153,7 @@ export class RuntimeMessageInjector {
     clearTimeout(entry.timer);
     this.pending.delete(correlationId);
 
-    if (accepted) {
-      try {
-        this.deps.db.markAgentInboxDelivered(entry.recipientAgentId, [entry.message.id]);
-      } catch (error) {
-        this.deps.logger.warn(
-          `[injector] markAgentInboxDelivered failed for ${entry.message.id}: ${error instanceof Error ? error.message : String(error)}`,
-        );
-      }
-      return;
-    }
+    if (accepted) return;
 
     this.deps.logger.warn(
       `[injector] steer rejected (${source}) for message ${entry.message.id} to agent ${entry.recipientAgentId}; falling back to wake + inbox projection`,

src/main/database.ts

@@ -20,7 +20,6 @@ export class AppDatabase extends AppDatabaseBase {
   searchMessages(companyId: string, query: string, opts?: { channel?: string; channelTargetId?: string | null; limit?: number }) { return this.messages.searchMessages(companyId, query, opts); }
   markMessageReadForReader(messageId: string, companyId: string, readerAgentId?: string | null) { return this.messages.markMessageReadForReader(messageId, companyId, readerAgentId); }
   listAgentInboxUnread(companyId: string, agentId: string) { return this.messages.listAgentInboxUnread(companyId, agentId); }
-  markAgentInboxDelivered(agentId: string, messageIds: string[]) { return this.messages.markAgentInboxDelivered(agentId, messageIds); }
 
   // ─── Social & Browser Actions ──────────────────────────────────────────────
 

src/main/database/messages.ts

@@ -339,28 +339,5 @@ export function buildMessageMethods(
       });
     },
 
-    /**
-     * Transactionally mark a batch of messages as delivered to `agentId`.
-     * - Direct messages: sets agent_messages.read_at = now() if currently null.
-     * - All messages (direct + channel): insert into agent_message_reads with
-     *   ON CONFLICT DO NOTHING so reprocessing is idempotent.
-     */
-    markAgentInboxDelivered(agentId: string, messageIds: string[]): void {
-      if (messageIds.length === 0) return;
-      const ts = nowIso();
-      deps.transaction(() => {
-        const db = getDb();
-        const directUpdate = db.prepare(
-          "update agent_messages set read_at = ? where id = ? and to_agent_id = ? and read_at is null",
-        );
-        const receiptInsert = db.prepare(
-          "insert into agent_message_reads (message_id, agent_id, read_at) values (?, ?, ?) on conflict(message_id, agent_id) do nothing",
-        );
-        for (const id of messageIds) {
-          directUpdate.run(ts, id, agentId);
-          receiptInsert.run(id, agentId, ts);
-        }
-      });
-    },
   };
 }