@@ -0,0 +1,6 @@
+import { Effect } from "effect"
+
+// Shared reconcile cell: McpTool registers its reconcile function here during
+// layer construction so the MCP service can await it after mutations without
+// introducing a circular layer dependency (McpTool depends on Mcp).
+export const cell: { reconcile: Effect.Effect<void, never, never> | null } = { reconcile: null }
@@ -13,6 +13,7 @@ import { Bus } from "../bus.js"
 import { Environment } from "../environment/index.js"
 import { Form } from "../form.js"
 import { Integration } from "../integration.js"
+import { cell as mcpReconcileCell } from "../mcp-reconcile.js"
 import { KeyedMutex } from "../effect/keyed-mutex.js"
 import { Location } from "../location.js"
 import { waitForAbort } from "@opencode/util/process"
@@ -636,6 +637,9 @@ export const layer = (options?: Options) =>
           const name = ServerName.make(server)
           overrides.set(name, config)
           yield* state.reload()
+          // Await tool registry reconciliation so a subsequent session/tool
+          // snapshot reflects the mutation (see #39902).
+          if (mcpReconcileCell.reconcile) yield* mcpReconcileCell.reconcile
         }),
         connect: Effect.fn("MCP.connect")(function* (server) {
           const name = ServerName.make(server)
@@ -644,6 +648,7 @@ export const layer = (options?: Options) =>
             yield* stopServer(name, target.entry)
             yield* startServer(name, target.entry)
           }).pipe(locks.withLock(name))
+          if (mcpReconcileCell.reconcile) yield* mcpReconcileCell.reconcile
         }),
         disconnect: Effect.fn("MCP.disconnect")(function* (server) {
           const name = ServerName.make(server)
@@ -653,12 +658,14 @@ export const layer = (options?: Options) =>
             target.entry.status = { status: "disabled" }
             yield* bus.publish(McpEvent.StatusChanged, { server: name })
           }).pipe(locks.withLock(name))
+          if (mcpReconcileCell.reconcile) yield* mcpReconcileCell.reconcile
         }),
         remove: Effect.fn("MCP.remove")(function* (server) {
           const name = ServerName.make(server)
           yield* requireServer(name)
           overrides.set(name, false)
           yield* state.reload()
+          if (mcpReconcileCell.reconcile) yield* mcpReconcileCell.reconcile
         }),
         // Reads report what is connected now; servers still starting contribute once they publish a change.
         tools: Effect.fn("MCP.tools")(function* () {
 
@@ -1,5 +1,7 @@
 export * as McpTool from "./mcp.js"
 
+import { cell as McpReconcile } from "../mcp-reconcile.js"
+
 import { ToolFailure } from "@opencode/ai"
 import { McpEvent } from "@opencode/schema/mcp-event"
 import { Context, Effect, Fiber, type JsonSchema, Layer, PubSub, Semaphore, Stream } from "effect"
@@ -19,6 +21,8 @@ export const name = (server: string, tool: string) => `${namespace(server)}_${to
 export interface Interface {
   /** Wait for the initial MCP tool registration to settle. */
   readonly flush: Effect.Effect<void>
+  /** Reconcile MCP tools into the ToolRegistry after a mutation. */
+  readonly reconcile: Effect.Effect<void>
 }
 
 export class Service extends Context.Service<Service, Interface>()("@opencode/McpTool") {}
@@ -127,6 +131,8 @@ export const layer = Layer.effect(
         yield* tools.reload()
       }),
     )
+    // Register for the MCP service to await after mutations.
+    McpReconcile.reconcile = reconcile
 
     // Servers announce tools in bursts and each read loads the whole catalog, so settle and refresh
     // once. The bus subscription stays eager; only the already-open sliding subscription is debounced.
@@ -141,7 +147,7 @@ export const layer = Layer.effect(
       Stream.runForEach(() => reconcile),
       Effect.forkScoped({ startImmediately: true }),
     )
-    return Service.of({ flush: Effect.asVoid(Fiber.await(initial)) })
+    return Service.of({ flush: Effect.asVoid(Fiber.await(initial)), reconcile })
   }),
 )