diff --git a/AGENTS.md b/AGENTS.md
index 7371a1be0..65ed0df61 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -129,8 +129,8 @@ Release commits are the exception: keep using `Release v0.x.y`.
 - Registries (`registry*.ts`) assemble tool sets. Add new tools to the appropriate registry so AI chat, MCP, and CLI eval paths can see them.
 - AI adapter (`packages/core/src/tools/ai-adapter.ts`) converts ToolDefs to Vercel AI tools with valibot schemas. `src/app/ai/tools/index.ts` is a thin app wire that creates `FigmaAPI` from the active editor.
 - CLI commands in `packages/cli/src/commands/**` are not generated from ToolDefs; they own CLI UX, pagination, and agentfmt formatting. The `eval` command exposes ToolDef operations through `FigmaAPI`.
-- MCP server code lives under `packages/mcp/src/`. MCP-only tools such as `open_file`, `new_document`, `save_file`, and `get_codegen_prompt` are registered in `tool/registration.ts` because they need server filesystem access or are not scene-graph tools.
-- Local MCP transport discovery lives under `packages/mcp/src/transport/`: macOS/Linux prefer an owner-only Unix socket, Windows uses localhost TCP, and `mcp.json` advertises the active transport and token. Keep test discovery paths isolated from the user's runtime file.
+- MCP server code lives under `packages/mcp/src/`. MCP-only tools such as `open_file`, `new_document`, `save_file`, and `get_codegen_prompt` are registered in `tool/registration.ts` because they need server filesystem access or are not scene-graph tools. Listener lifecycle and session ownership live under `src/server/`; the stdio client bridge lives under `src/stdio/`.
+- Local MCP transport discovery lives under `packages/mcp/src/transport/`: macOS/Linux prefer an owner-only Unix socket, Windows uses localhost TCP, and `mcp.json` advertises the active transport and token. Keep transport tests grouped under `tests/engine/mcp/{server,stdio,transport}/`, shared MCP fixtures under `tests/helpers/mcp/`, and test discovery paths isolated from the user's runtime file.
 - `open_file` and `new_document` are only registered when `OPENPENCIL_MCP_ROOT` is set. Export tools can write files under that root when given a `path`; path checks must resolve symlinks before filesystem access.
 - Core codegen prompts live as markdown under `packages/core/src/tools/prompts/`; app chat/ACP prompts live under `src/app/ai/**` markdown files.
 - `FigmaAPI` (`packages/core/src/figma-api/`) is the execution target for tools and CLI eval. It is Figma Plugin API compatible and uses Symbols for hidden internals.
diff --git a/bunfig.toml b/bunfig.toml
index 6746ee7ae..5ddc325e3 100644
--- a/bunfig.toml
+++ b/bunfig.toml
@@ -2,6 +2,6 @@
 # Preload discovery-file isolation for every `bun test` run so engine tests
 # never clobber the real ~/Library/Application Support/OpenPencil/mcp.json
 # (which would break a running OpenPencil desktop app). See
-# tests/helpers/mcp-discovery-isolation.ts for the rationale.
+# tests/helpers/mcp/discovery-isolation.ts for the rationale.
 [test]
-preload = ["./tests/helpers/mcp-discovery-isolation.ts"]
+preload = ["./tests/helpers/mcp/discovery-isolation.ts"]
diff --git a/packages/mcp/src/server.ts b/packages/mcp/src/server.ts
index a5cd47ad9..bac648467 100644
--- a/packages/mcp/src/server.ts
+++ b/packages/mcp/src/server.ts
@@ -13,7 +13,7 @@ import { createBrowserRpcBridge } from '#mcp/browser-rpc'
 import { MCP_CORS_HEADERS, MCP_CORS_METHODS, MCP_EXPOSED_HEADERS } from '#mcp/http-options'
 import type { RpcJsonObject } from '#mcp/json'
 import { preprocessRpc } from '#mcp/jsx-preprocess'
-import { createMcpSessionManager } from '#mcp/mcp-sessions'
+import { createMcpSessionManager } from '#mcp/server/sessions'
 import { registerTools } from '#mcp/tool/registration'
 
 import packageJson from '../package.json' with { type: 'json' }
@@ -26,7 +26,7 @@ import {
   teardownListeners,
   tryStartTcp,
   tryWriteDiscovery
-} from './lifecycle'
+} from './server/lifecycle'
 
 export const MCP_VERSION: string = packageJson.version
 
diff --git a/packages/mcp/src/lifecycle.ts b/packages/mcp/src/server/lifecycle.ts
similarity index 100%
rename from packages/mcp/src/lifecycle.ts
rename to packages/mcp/src/server/lifecycle.ts
diff --git a/packages/mcp/src/mcp-sessions.ts b/packages/mcp/src/server/sessions.ts
similarity index 100%
rename from packages/mcp/src/mcp-sessions.ts
rename to packages/mcp/src/server/sessions.ts
diff --git a/packages/mcp/src/stdio.ts b/packages/mcp/src/stdio.ts
index 953561749..c6c5f1be2 100644
--- a/packages/mcp/src/stdio.ts
+++ b/packages/mcp/src/stdio.ts
@@ -3,7 +3,7 @@ import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js'
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
 
 import { MCP_VERSION, registerTools } from '#mcp/server'
-import { createStdioRpcBridge } from '#mcp/stdio-bridge'
+import { createStdioRpcBridge } from '#mcp/stdio/bridge'
 
 if (process.argv.includes('--help') || process.argv.includes('-h')) {
   process.stdout.write(
diff --git a/packages/mcp/src/stdio-bridge.ts b/packages/mcp/src/stdio/bridge.ts
similarity index 100%
rename from packages/mcp/src/stdio-bridge.ts
rename to packages/mcp/src/stdio/bridge.ts
diff --git a/tests/engine/mcp/browser-rpc.test.ts b/tests/engine/mcp/browser-rpc.test.ts
index d052bf3bb..6df4de98c 100644
--- a/tests/engine/mcp/browser-rpc.test.ts
+++ b/tests/engine/mcp/browser-rpc.test.ts
@@ -136,7 +136,7 @@ describe('BrowserRpcBridge reconnection', () => {
     servers.push(srv)
   }
 
-  test('pending requests from old browser are rejected on reconnect (Fix 1)', async () => {
+  test('rejects pending requests from a disconnected browser on reconnect', async () => {
     const pairA = await setupWsPair()
     track(pairA)
     const pairB = await setupWsPair()
@@ -166,7 +166,7 @@ describe('BrowserRpcBridge reconnection', () => {
     expect(elapsed).toBeLessThan(5_000)
   })
 
-  test('connection waiters survive handleClose and are NOT rejected (Fix 2)', async () => {
+  test('keeps connection waiters pending across browser reconnects', async () => {
     const pair = await setupWsPair()
     track(pair)
 
@@ -179,8 +179,8 @@ describe('BrowserRpcBridge reconnection', () => {
     await registerBrowser(pair.serverWs, pair.clientWs, bridge)
 
     // Close the client side — this should trigger serverWs 'close'
-    // which calls bridge.handleClose(). Fix 2 ensures that connection
-    // waiters are NOT rejected here.
+    // which calls bridge.handleClose(). Connection waiters must remain
+    // pending here.
     pair.clientWs.close()
     await new Promise<void>((resolve) => {
       setTimeout(resolve, 200)
diff --git a/tests/engine/mcp/lifecycle-failure.test.ts b/tests/engine/mcp/server/cleanup.test.ts
similarity index 99%
rename from tests/engine/mcp/lifecycle-failure.test.ts
rename to tests/engine/mcp/server/cleanup.test.ts
index a71631b4b..9d5a9e2df 100644
--- a/tests/engine/mcp/lifecycle-failure.test.ts
+++ b/tests/engine/mcp/server/cleanup.test.ts
@@ -5,7 +5,7 @@ import { join } from 'node:path'
 
 import { startServer, type ServerHandle } from '#mcp/server'
 
-import { socketRequest, type HealthResponse } from './helpers'
+import { socketRequest, type HealthResponse } from '#tests/helpers/mcp/server'
 
 const isUnix = process.platform !== 'win32'
 const SOCKET_DIR = join(tmpdir(), `openpencil-test-lifecycle-${process.pid}`)
diff --git a/tests/engine/mcp/server.test.ts b/tests/engine/mcp/server/index.test.ts
similarity index 99%
rename from tests/engine/mcp/server.test.ts
rename to tests/engine/mcp/server/index.test.ts
index b79bce59d..4107c0558 100644
--- a/tests/engine/mcp/server.test.ts
+++ b/tests/engine/mcp/server/index.test.ts
@@ -15,7 +15,7 @@ import {
   waitForBrowserRegistration,
   type HealthResponse,
   type MockBrowser
-} from './helpers'
+} from '#tests/helpers/mcp/server'
 
 const isUnix = process.platform !== 'win32'
 const SOCKET_DIR = join(tmpdir(), `openpencil-test-server-${process.pid}`)
diff --git a/tests/engine/mcp/server-auth.test.ts b/tests/engine/mcp/server/security.test.ts
similarity index 99%
rename from tests/engine/mcp/server-auth.test.ts
rename to tests/engine/mcp/server/security.test.ts
index 95e93fb0b..97d5f2f2e 100644
--- a/tests/engine/mcp/server-auth.test.ts
+++ b/tests/engine/mcp/server/security.test.ts
@@ -11,7 +11,11 @@ import { SceneGraph } from '@open-pencil/scene-graph'
 import { startServer, paramToZod } from '#mcp/server'
 import type { DiscoveryInfo } from '#mcp/transport/discovery'
 
-import { connectMockBrowser, waitForBrowserRegistration, type HealthResponse } from './helpers'
+import {
+  connectMockBrowser,
+  waitForBrowserRegistration,
+  type HealthResponse
+} from '#tests/helpers/mcp/server'
 
 const isUnix = process.platform !== 'win32'
 const SOCKET_DIR = join(tmpdir(), `openpencil-test-server-${process.pid}`)
diff --git a/tests/engine/mcp/server-transport.test.ts b/tests/engine/mcp/server/transport.test.ts
similarity index 99%
rename from tests/engine/mcp/server-transport.test.ts
rename to tests/engine/mcp/server/transport.test.ts
index dd121ec03..3fa6f1873 100644
--- a/tests/engine/mcp/server-transport.test.ts
+++ b/tests/engine/mcp/server/transport.test.ts
@@ -19,7 +19,7 @@ import {
   waitForBrowserRegistration,
   type HealthResponse,
   type MockBrowser
-} from './helpers'
+} from '#tests/helpers/mcp/server'
 
 const isUnix = process.platform !== 'win32'
 const SOCKET_DIR = join(tmpdir(), `openpencil-test-server-${process.pid}`)
diff --git a/tests/engine/mcp/stdio-auth.test.ts b/tests/engine/mcp/stdio/auth.test.ts
similarity index 98%
rename from tests/engine/mcp/stdio-auth.test.ts
rename to tests/engine/mcp/stdio/auth.test.ts
index 754183d49..d1009c6c0 100644
--- a/tests/engine/mcp/stdio-auth.test.ts
+++ b/tests/engine/mcp/stdio/auth.test.ts
@@ -5,7 +5,7 @@ import { createServer, type Server } from 'node:http'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 
-import { createStdioRpcBridge } from '#mcp/stdio-bridge'
+import { createStdioRpcBridge } from '#mcp/stdio/bridge'
 
 const TEST_DIR = join(tmpdir(), `openpencil-test-stdio-auth-${process.pid}`)
 const TEST_SOCKET = join(TEST_DIR, 'mcp-test.sock')
@@ -130,7 +130,7 @@ async function createBridgeAndWaitForReady(
 
 const isUnix = process.platform !== 'win32'
 
-describe.skipIf(!isUnix)('Fix 4 - Auth token auto-discovery and transparent retry', () => {
+describe.skipIf(!isUnix)('MCP stdio authentication', () => {
   let httpServer: Server | null = null
   let bridges: Array<ReturnType<typeof createStdioRpcBridge>> = []
   const origSocketEnv = process.env.OPENPENCIL_MCP_SOCKET
diff --git a/tests/engine/mcp/stdio.test.ts b/tests/engine/mcp/stdio/index.test.ts
similarity index 99%
rename from tests/engine/mcp/stdio.test.ts
rename to tests/engine/mcp/stdio/index.test.ts
index 17d2da3db..21297a8a6 100644
--- a/tests/engine/mcp/stdio.test.ts
+++ b/tests/engine/mcp/stdio/index.test.ts
@@ -11,8 +11,11 @@ import { SceneGraph } from '@open-pencil/scene-graph'
 import { startServer, type ServerHandle } from '#mcp/server'
 
 import { expectDefined, getNodeOrThrow } from '#tests/helpers/assert'
-
-import { connectMockBrowser, waitForBrowserRegistration, type MockBrowser } from './helpers'
+import {
+  connectMockBrowser,
+  waitForBrowserRegistration,
+  type MockBrowser
+} from '#tests/helpers/mcp/server'
 
 const AUTH_TOKEN = 'test-stdio-token'
 const NO_DOCUMENT_AUTH_TOKEN = 'test-stdio-no-document-token'
diff --git a/tests/engine/mcp/stdio-bridge-reconnect.test.ts b/tests/engine/mcp/stdio/reconnect.test.ts
similarity index 99%
rename from tests/engine/mcp/stdio-bridge-reconnect.test.ts
rename to tests/engine/mcp/stdio/reconnect.test.ts
index 896da7725..d663c07ed 100644
--- a/tests/engine/mcp/stdio-bridge-reconnect.test.ts
+++ b/tests/engine/mcp/stdio/reconnect.test.ts
@@ -5,7 +5,7 @@ import { createServer, type Server } from 'node:http'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 
-import { createStdioRpcBridge } from '#mcp/stdio-bridge'
+import { createStdioRpcBridge } from '#mcp/stdio/bridge'
 import { getDiscoveryPath } from '#mcp/transport/paths'
 
 const isUnix = process.platform !== 'win32'
diff --git a/tests/engine/mcp/discovery-isolation.test.ts b/tests/engine/mcp/test-support/discovery-isolation.test.ts
similarity index 92%
rename from tests/engine/mcp/discovery-isolation.test.ts
rename to tests/engine/mcp/test-support/discovery-isolation.test.ts
index 90c2e8f28..0fd46f5a1 100644
--- a/tests/engine/mcp/discovery-isolation.test.ts
+++ b/tests/engine/mcp/test-support/discovery-isolation.test.ts
@@ -1,8 +1,8 @@
 import { describe, expect, it } from 'bun:test'
 
-import { isAliveFromKillError, isProcessAlive } from '#tests/helpers/mcp-discovery-isolation'
+import { isAliveFromKillError, isProcessAlive } from '#tests/helpers/mcp/discovery-isolation'
 
-describe('mcp-discovery-isolation > isProcessAlive', () => {
+describe('MCP test discovery isolation', () => {
   it('returns true for the current (live) process', () => {
     // The stale-dir sweep must never treat the running process as dead.
     expect(isProcessAlive(process.pid)).toBe(true)
diff --git a/tests/engine/mcp/transport.test.ts b/tests/engine/mcp/transport/paths.test.ts
similarity index 99%
rename from tests/engine/mcp/transport.test.ts
rename to tests/engine/mcp/transport/paths.test.ts
index ea1804eff..3d0dc1a21 100644
--- a/tests/engine/mcp/transport.test.ts
+++ b/tests/engine/mcp/transport/paths.test.ts
@@ -124,7 +124,7 @@ describe('transport/paths', () => {
   })
 
   describe('getDiscoveryPath', () => {
-    // The test preload (tests/helpers/mcp-discovery-isolation.ts) sets
+    // The test preload (tests/helpers/mcp/discovery-isolation.ts) sets
     // OPENPENCIL_MCP_DISCOVERY_PATH to a per-process temp path. Each case
     // below saves/clears/restores both env vars so platform-default behavior
     // can be asserted independently of the preload.
diff --git a/tests/helpers/mcp-discovery-isolation.ts b/tests/helpers/mcp/discovery-isolation.ts
similarity index 100%
rename from tests/helpers/mcp-discovery-isolation.ts
rename to tests/helpers/mcp/discovery-isolation.ts
diff --git a/tests/engine/mcp/helpers.ts b/tests/helpers/mcp/server.ts
similarity index 100%
rename from tests/engine/mcp/helpers.ts
rename to tests/helpers/mcp/server.ts