diff --git a/src/agent/message-client-skills.test.ts b/src/agent/message-client-skills.test.ts
index 55cad6846..0f2a966ea 100644
--- a/src/agent/message-client-skills.test.ts
+++ b/src/agent/message-client-skills.test.ts
@@ -1,5 +1,9 @@
 import { describe, expect, test } from "bun:test";
-import { buildConversationMessagesCreateRequestBody } from "@/agent/message";
+import {
+  buildConversationMessagesCreateRequestBody,
+  sendMessageStreamWithBackend,
+} from "@/agent/message";
+import type { Backend } from "@/backend";
 
 describe("buildConversationMessagesCreateRequestBody client_skills", () => {
   test("includes client_skills alongside client_tools", () => {
@@ -32,4 +36,46 @@ describe("buildConversationMessagesCreateRequestBody client_skills", () => {
       },
     ]);
   });
+
+  test("an explicit empty runtime skill scope sends no client skills on every turn", async () => {
+    const requestBodies: Array<{ client_skills?: unknown[] }> = [];
+    const emptyStream = {
+      [Symbol.asyncIterator]() {
+        return {
+          next: async () => ({ done: true as const, value: undefined }),
+        };
+      },
+    };
+    const backend = {
+      createConversationMessageStream: async (
+        _conversationId: string,
+        body: { client_skills?: unknown[] },
+      ) => {
+        requestBodies.push(body);
+        return emptyStream;
+      },
+    } as unknown as Backend;
+    const preparedToolContext = {
+      contextId: "no-skills-context",
+      clientTools: [],
+      loadedToolNames: [],
+    };
+
+    for (const content of ["initial reflection", "continued reflection"]) {
+      await sendMessageStreamWithBackend(
+        backend,
+        "conv-reflector",
+        [{ type: "message", role: "user", content }],
+        {
+          agentId: "agent-reflector",
+          preparedToolContext,
+          skillSources: [],
+          skipImageNormalization: true,
+        },
+      );
+    }
+
+    expect(requestBodies).toHaveLength(2);
+    expect(requestBodies.map((body) => body.client_skills)).toEqual([[], []]);
+  });
 });
diff --git a/src/agent/message.ts b/src/agent/message.ts
index a1eb7bd82..c3e6a53ce 100644
--- a/src/agent/message.ts
+++ b/src/agent/message.ts
@@ -10,6 +10,7 @@ import type {
   LettaStreamingResponse,
 } from "@letta-ai/letta-client/resources/agents/messages";
 import type { MessageCreateParams as ConversationMessageCreateParams } from "@letta-ai/letta-client/resources/conversations/messages";
+import type { SkillSource } from "@/agent/skill-sources";
 import { type Backend, getBackend } from "@/backend";
 import {
   type ClientTool,
@@ -196,6 +197,8 @@ export type SendMessageStreamOptions = {
   overrideModel?: string;
   /** Explicit turn-scoped tool snapshot. When present, bypasses the global registry. */
   preparedToolContext?: PreparedToolExecutionContext;
+  /** Turn-scoped skill roots. [] disables all client skill discovery. */
+  skillSources?: SkillSource[];
   /**
    * Allow sending a cached previous response id for this request. Callers should
    * set this only for approval continuations that were fully auto-handled by
@@ -321,7 +324,7 @@ export async function sendMessageStreamWithBackend(
   const { clientSkills, errors: clientSkillDiscoveryErrors } =
     await buildClientSkillsPayload({
       agentId: opts.agentId,
-      skillSources: getSkillSources(),
+      skillSources: opts.skillSources ?? getSkillSources(),
     });
 
   const resolvedConversationId = conversationId;
diff --git a/src/app-server-client.test.ts b/src/app-server-client.test.ts
index aa0f1c9d4..51fcc299b 100644
--- a/src/app-server-client.test.ts
+++ b/src/app-server-client.test.ts
@@ -123,12 +123,14 @@ describe("app-server client", () => {
     const responsePromise = client.runtimeStart({
       create_agent: { body: { name: "SDK test" } },
       create_conversation: { body: {} },
+      skill_sources: [],
     });
 
     expect(JSON.parse(control.sent[0] ?? "{}")).toMatchObject({
       type: "runtime_start",
       request_id: "runtime-start-1",
       create_agent: { body: { name: "SDK test" } },
+      skill_sources: [],
     });
 
     control.receive({
diff --git a/src/tools/toolset.ts b/src/tools/toolset.ts
index 363352c5b..0ef616992 100644
--- a/src/tools/toolset.ts
+++ b/src/tools/toolset.ts
@@ -1,5 +1,6 @@
 import type { AgentState } from "@letta-ai/letta-client/resources/agents/agents";
 import { resolveModel } from "@/agent/model";
+import type { SkillSource } from "@/agent/skill-sources";
 import { getBackend } from "@/backend";
 import { getClient } from "@/backend/api/client";
 import type { MessageChannelToolDiscoveryScope } from "@/channels/message-tool";
@@ -443,6 +444,7 @@ export async function prepareToolExecutionContextForScope(params: {
   workingDirectory?: string;
   permissionModeState?: PermissionModeState;
   cachedAgent?: AgentState | null;
+  skillSources?: SkillSource[];
   channelTurnSources?: import("@/channels/types").ChannelTurnSource[];
   modContext?: ModContext;
   modEvents?: ModEvents;
@@ -459,6 +461,7 @@ export async function prepareToolExecutionContextForScope(params: {
     workingDirectory,
     permissionModeState,
     cachedAgent,
+    skillSources,
     channelTurnSources: explicitChannelTurnSources,
     modContext,
     modEvents,
@@ -541,6 +544,7 @@ export async function prepareToolExecutionContextForScope(params: {
       agentName: (agent as AgentState).name ?? null,
       conversationId: scopedConversationId,
       workingDirectory,
+      ...(skillSources !== undefined ? { skillSources } : {}),
       ...(channelToolScope.channels.length > 0 ? { channelToolScope } : {}),
       ...(inheritedChannelTurnSources.length > 0
         ? { channelTurnSources: inheritedChannelTurnSources }
diff --git a/src/types/protocol_v2.ts b/src/types/protocol_v2.ts
index 89f822a62..2099de67e 100644
--- a/src/types/protocol_v2.ts
+++ b/src/types/protocol_v2.ts
@@ -30,6 +30,7 @@ import type {
   MessageListParams,
 } from "@letta-ai/letta-client/resources/conversations/messages";
 import type { StopReasonType } from "@letta-ai/letta-client/resources/runs/runs";
+import type { SkillSource } from "@/agent/skill-sources";
 
 export type DmPolicy = "pairing" | "allowlist" | "open";
 
@@ -830,6 +831,8 @@ export interface RuntimeStartCommand {
   cwd?: string | null;
   /** Initial permission mode for this runtime scope. */
   mode?: DevicePermissionMode;
+  /** Skill roots enabled for this runtime. An empty array disables all skills. */
+  skill_sources?: readonly SkillSource[];
   /** Optional client metadata for diagnostics/future protocol negotiation. */
   client_info?: RuntimeStartClientInfo;
   /** Whether to probe backend state for stale pending approvals before replaying state. Defaults to true. */
diff --git a/src/websocket/listen-client-protocol.test.ts b/src/websocket/listen-client-protocol.test.ts
index 9c4004a7d..00767b65d 100644
--- a/src/websocket/listen-client-protocol.test.ts
+++ b/src/websocket/listen-client-protocol.test.ts
@@ -605,6 +605,7 @@ describe("listen-client parseServerMessage", () => {
             },
             cwd: cwdDir,
             mode: "acceptEdits",
+            skill_sources: [],
             recover_approvals: false,
           },
           socket as unknown as WebSocket,
@@ -636,6 +637,12 @@ describe("listen-client parseServerMessage", () => {
             runtimeScope.conversation_id,
           ),
         ).toBe(cwdDir);
+        const scopedRuntime = [...listener.conversationRuntimes.values()].find(
+          (candidate) =>
+            candidate.agentId === runtimeScope.agent_id &&
+            candidate.conversationId === runtimeScope.conversation_id,
+        );
+        expect(scopedRuntime?.skillSources).toEqual([]);
         expect(messages).toEqual(
           expect.arrayContaining([
             expect.objectContaining({
diff --git a/src/websocket/listener/commands/runtime-start.ts b/src/websocket/listener/commands/runtime-start.ts
index e094fb263..a970705ce 100644
--- a/src/websocket/listener/commands/runtime-start.ts
+++ b/src/websocket/listener/commands/runtime-start.ts
@@ -142,10 +142,10 @@ async function resolveRuntimeStartAgent(
       : parsed.create_agent.body;
     const agent = await backend.createAgent(body);
     if (withMemfs) {
-      // Finish memfs setup (settings, repo clone, legacy tool detach) without
-      // blocking runtime start. The tag is already stamped at creation, so
-      // lazy sync paths can complete this even if the process dies here.
-      void enableMemfsIfCloud(agent.id);
+      // runtime_start is a readiness boundary for SDK callers. Do not return
+      // the created agent while its MemFS clone can still replace the working
+      // tree: callers may seed and commit files immediately after startup.
+      await enableMemfsIfCloud(agent.id);
     } else {
       // Worker-style agent: no memfs of its own; a memory scope may be
       // provided per session (MEMORY_DIR + LETTA_MEMORY_DIR_EXPLICIT).
@@ -197,6 +197,11 @@ async function applyRuntimeStartState(
   scope: RuntimeScope,
   scopedRuntime: ConversationRuntime,
 ): Promise<void> {
+  // runtime_start is authoritative for this app-server session. Reset to the
+  // harness defaults when omitted; preserve [] as an explicit no-skills scope.
+  scopedRuntime.skillSources =
+    parsed.skill_sources !== undefined ? [...parsed.skill_sources] : null;
+
   if (parsed.mode) {
     const mode = migratePermissionMode(parsed.mode);
     if (!mode) {
diff --git a/src/websocket/listener/protocol-inbound.test.ts b/src/websocket/listener/protocol-inbound.test.ts
index d385d87c4..bd0aa4741 100644
--- a/src/websocket/listener/protocol-inbound.test.ts
+++ b/src/websocket/listener/protocol-inbound.test.ts
@@ -29,6 +29,7 @@ describe("agent/conversation management protocol-inbound validators", () => {
       create_conversation: { body: { summary: "New conversation" } },
       cwd: "/tmp/project",
       mode: "acceptEdits",
+      skill_sources: [],
       client_info: { name: "test", title: "Test", version: "1.0.0" },
       external_tools: [
         {
@@ -122,6 +123,12 @@ describe("agent/conversation management protocol-inbound validators", () => {
       agent_id: "agent-1",
       mode: "bad",
     },
+    {
+      type: "runtime_start",
+      request_id: "r0",
+      agent_id: "agent-1",
+      skill_sources: ["unknown"],
+    },
     {
       type: "runtime_start",
       request_id: "r0",
diff --git a/src/websocket/listener/protocol-inbound.ts b/src/websocket/listener/protocol-inbound.ts
index 86696678a..aceeffe6d 100644
--- a/src/websocket/listener/protocol-inbound.ts
+++ b/src/websocket/listener/protocol-inbound.ts
@@ -461,6 +461,7 @@ export function isRuntimeStartCommand(
     create_conversation?: unknown;
     cwd?: unknown;
     mode?: unknown;
+    skill_sources?: unknown;
     client_info?: unknown;
     recover_approvals?: unknown;
     force_device_status?: unknown;
@@ -478,6 +479,15 @@ export function isRuntimeStartCommand(
       isRuntimeStartCreateConversationOptions(c.create_conversation)) &&
     (c.cwd === undefined || c.cwd === null || typeof c.cwd === "string") &&
     (c.mode === undefined || isDevicePermissionMode(c.mode)) &&
+    (c.skill_sources === undefined ||
+      (Array.isArray(c.skill_sources) &&
+        c.skill_sources.every(
+          (source) =>
+            source === "bundled" ||
+            source === "global" ||
+            source === "agent" ||
+            source === "project",
+        ))) &&
     (c.client_info === undefined || isRuntimeStartClientInfo(c.client_info)) &&
     (c.recover_approvals === undefined ||
       typeof c.recover_approvals === "boolean") &&
diff --git a/src/websocket/listener/recovery.ts b/src/websocket/listener/recovery.ts
index 63d9cf086..1dc8b7533 100644
--- a/src/websocket/listener/recovery.ts
+++ b/src/websocket/listener/recovery.ts
@@ -691,6 +691,9 @@ export async function resolveRecoveredApprovalResponse(
       recovered.conversationId,
     ),
     modEvents: ensureListenerModAdapter(runtime.listener).events,
+    ...(runtime.skillSources !== null
+      ? { skillSources: runtime.skillSources }
+      : {}),
   });
   runtime.currentToolset = preparedToolContext.toolset;
   runtime.currentToolsetPreference = preparedToolContext.toolsetPreference;
diff --git a/src/websocket/listener/runtime.ts b/src/websocket/listener/runtime.ts
index 06d6e6544..b68cc3a00 100644
--- a/src/websocket/listener/runtime.ts
+++ b/src/websocket/listener/runtime.ts
@@ -159,6 +159,7 @@ export function createConversationRuntime(
     key: runtimeKey,
     agentId: normalizedAgentId,
     conversationId: normalizedConversationId,
+    skillSources: null,
     activeChannelTurnSources: null,
     activeChannelTurnBatchId: null,
     activeChannelTurnContextRecovered: false,
diff --git a/src/websocket/listener/turn.ts b/src/websocket/listener/turn.ts
index 602a97fb3..ca1e7d68c 100644
--- a/src/websocket/listener/turn.ts
+++ b/src/websocket/listener/turn.ts
@@ -720,6 +720,9 @@ export async function handleIncomingMessage(
       workingDirectory: turnWorkingDirectory,
       permissionModeState: turnPermissionModeState,
       cachedAgent,
+      ...(runtime.skillSources !== null
+        ? { skillSources: runtime.skillSources }
+        : {}),
       channelTurnSources: msg.channelTurnSources,
       modEvents: ensureListenerModAdapter(runtime.listener).events,
     });
@@ -734,6 +737,9 @@ export async function handleIncomingMessage(
       workingDirectory: turnWorkingDirectory,
       permissionModeState: turnPermissionModeState,
       preparedToolContext: preparedToolContext.preparedToolContext,
+      ...(runtime.skillSources !== null
+        ? { skillSources: runtime.skillSources }
+        : {}),
       skipImageNormalization: true,
       ...(providerFallback.overrideModel
         ? { overrideModel: providerFallback.overrideModel }
diff --git a/src/websocket/listener/types.ts b/src/websocket/listener/types.ts
index 30a63417a..850423366 100644
--- a/src/websocket/listener/types.ts
+++ b/src/websocket/listener/types.ts
@@ -5,6 +5,7 @@ import type {
   ApprovalDecision,
   ApprovalResult,
 } from "@/agent/approval-execution";
+import type { SkillSource } from "@/agent/skill-sources";
 import type { ChannelTurnProgressBuilder } from "@/channels/progress";
 import type { ChannelTurnSource } from "@/channels/types";
 import type { ContextTracker } from "@/cli/helpers/context-tracker";
@@ -140,6 +141,8 @@ export type ConversationRuntime = {
   key: string;
   agentId: string | null;
   conversationId: string;
+  /** Runtime-start override; null means use the normal harness defaults. */
+  skillSources: SkillSource[] | null;
   activeChannelTurnSources: ChannelTurnSource[] | null;
   activeChannelTurnBatchId: string | null;
   activeChannelTurnContextRecovered?: boolean;