diff --git a/common/eslint-config/eslint.config.mjs b/common/eslint-config/eslint.config.mjs
index fb0b5d3db6..808fe1729d 100644
--- a/common/eslint-config/eslint.config.mjs
+++ b/common/eslint-config/eslint.config.mjs
@@ -94,6 +94,11 @@ export default defineConfig(
             'no-console': 'off'
         }
     },
+    {
+        // Ignore build artifacts everywhere (mirrors .prettierignore). A flat-config
+        // object with only `ignores` is a global ignore; ESLint does not skip dist by default.
+        ignores: ['**/dist/**', '**/build/**', '**/coverage/**']
+    },
     {
         // Ignore generated protocol types everywhere
         ignores: ['**/spec.types.2025-11-25.ts', '**/spec.types.2026-07-28.ts']
diff --git a/docs/.vitepress/config.mts b/docs/.vitepress/config.mts
index f99c9bcb8f..551575032d 100644
--- a/docs/.vitepress/config.mts
+++ b/docs/.vitepress/config.mts
@@ -4,8 +4,14 @@ import { fileURLToPath } from 'node:url';
 
 import { defineConfig, type DefaultTheme } from 'vitepress';
 
+import { generateLlmsArtifacts } from './llms';
+import { guideSidebar } from './nav';
+
 const docsDir = resolve(dirname(fileURLToPath(import.meta.url)), '..');
 
+/** Absolute site URL (origin + base), the single copy every consumer derives from. */
+const siteUrl = 'https://ts.sdk.modelcontextprotocol.io/v2';
+
 /**
  * The API Reference sidebar is generated by `pnpm docs:api` (typedoc + typedoc-vitepress-theme)
  * into docs/api/typedoc-sidebar.json. When it is missing (e.g. `docs:dev` before `docs:api`),
@@ -25,7 +31,7 @@ export default defineConfig({
     description: 'The TypeScript SDK implementation of the Model Context Protocol specification.',
     base: '/v2/',
     srcExclude: ['v1/**', '_meta/**', 'behavior-surface-pins.md'],
-    sitemap: { hostname: 'https://ts.sdk.modelcontextprotocol.io/v2/' },
+    sitemap: { hostname: `${siteUrl}/` },
     markdown: {
         config(md) {
             // Spec-generated JSDoc (packages/core-internal/src/types/spec.types.*.ts) carries
@@ -42,6 +48,9 @@ export default defineConfig({
             };
         }
     },
+    buildEnd(siteConfig) {
+        generateLlmsArtifacts(docsDir, siteConfig.outDir, siteUrl);
+    },
     themeConfig: {
         nav: [
             { text: 'Get started', link: '/get-started/first-server', activeMatch: '^/get-started/' },
@@ -52,82 +61,7 @@ export default defineConfig({
             { text: 'V1 Docs', link: 'https://ts.sdk.modelcontextprotocol.io/' }
         ],
         sidebar: [
-            {
-                text: 'Get started',
-                items: [
-                    { text: 'Build a server', link: '/get-started/first-server' },
-                    { text: 'Plug into a real host', link: '/get-started/real-host' },
-                    { text: 'Build a client', link: '/get-started/first-client' },
-                    { text: 'Packages', link: '/get-started/packages' },
-                    { text: 'Examples', link: '/get-started/examples' }
-                ]
-            },
-            {
-                text: 'Servers',
-                items: [
-                    { text: 'Tools', link: '/servers/tools' },
-                    { text: 'Resources', link: '/servers/resources' },
-                    { text: 'Prompts', link: '/servers/prompts' },
-                    { text: 'Completion', link: '/servers/completion' },
-                    { text: 'Logging, progress, cancellation', link: '/servers/logging-progress-cancellation' },
-                    { text: 'Elicitation', link: '/servers/elicitation' },
-                    { text: 'Sampling (sunset)', link: '/servers/sampling' },
-                    { text: 'Input required', link: '/servers/input-required' },
-                    { text: 'Notifications', link: '/servers/notifications' },
-                    { text: 'Errors', link: '/servers/errors' }
-                ]
-            },
-            {
-                text: 'Serving',
-                items: [
-                    { text: 'stdio', link: '/serving/stdio' },
-                    { text: 'HTTP', link: '/serving/http' },
-                    { text: 'Express', link: '/serving/express' },
-                    { text: 'Hono', link: '/serving/hono' },
-                    { text: 'Fastify', link: '/serving/fastify' },
-                    { text: 'Web-standard runtimes', link: '/serving/web-standard' },
-                    { text: 'Sessions, state, scaling', link: '/serving/sessions-state-scaling' },
-                    { text: 'Authorization', link: '/serving/authorization' },
-                    { text: 'Legacy clients', link: '/serving/legacy-clients' }
-                ]
-            },
-            {
-                text: 'Clients',
-                items: [
-                    { text: 'Connect', link: '/clients/connect' },
-                    { text: 'Calling', link: '/clients/calling' },
-                    { text: 'Handle server requests', link: '/clients/server-requests' },
-                    { text: 'Roots (sunset)', link: '/clients/roots' },
-                    { text: 'Subscriptions', link: '/clients/subscriptions' },
-                    { text: 'OAuth', link: '/clients/oauth' },
-                    { text: 'Machine auth', link: '/clients/machine-auth' },
-                    { text: 'Middleware', link: '/clients/middleware' },
-                    { text: 'Caching', link: '/clients/caching' }
-                ]
-            },
-            { text: 'Protocol versions', link: '/protocol-versions' },
-            {
-                text: 'Advanced',
-                collapsed: true,
-                items: [
-                    { text: 'Low-level server', link: '/advanced/low-level-server' },
-                    { text: 'Custom methods', link: '/advanced/custom-methods' },
-                    { text: 'Schema libraries', link: '/advanced/schema-libraries' },
-                    { text: 'Custom transports', link: '/advanced/custom-transports' },
-                    { text: 'Wire schemas', link: '/advanced/wire-schemas' },
-                    { text: 'Gateway', link: '/advanced/gateway' }
-                ]
-            },
-            { text: 'Testing', link: '/testing' },
-            { text: 'Troubleshooting', link: '/troubleshooting' },
-            {
-                text: 'Migration',
-                items: [
-                    { text: 'Overview', link: '/migration/' },
-                    { text: 'Upgrade to v2', link: '/migration/upgrade-to-v2' },
-                    { text: '2026-07-28 protocol support', link: '/migration/support-2026-07-28' }
-                ]
-            },
+            ...guideSidebar,
             {
                 text: 'API Reference',
                 collapsed: true,
diff --git a/docs/.vitepress/llms.ts b/docs/.vitepress/llms.ts
new file mode 100644
index 0000000000..af186fbac9
--- /dev/null
+++ b/docs/.vitepress/llms.ts
@@ -0,0 +1,213 @@
+import { mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { dirname, join, posix } from 'node:path';
+
+import type { DefaultTheme } from 'vitepress';
+
+import { guideSidebar } from './nav';
+
+/**
+ * LLM-facing renditions of the docs, generated into the site output at build
+ * time (wired into `buildEnd` in config.mts), following https://llmstxt.org
+ * and the Python SDK's equivalent:
+ *
+ * - `<page>.md` next to every guide page's HTML — the page as plain markdown,
+ *   frontmatter stripped, links absolutized (cross-page links point at the
+ *   `.md` renditions so an agent can keep fetching markdown).
+ * - `llms.txt` — the index: one line per page, grouped like the sidebar.
+ * - `llms-full.txt` — every guide page concatenated in sidebar order.
+ *
+ * The generated API reference stays out of all three (linked, not inlined):
+ * it would swamp the prose that answers most questions.
+ */
+
+interface Page {
+    /** Sidebar title. */
+    title: string;
+    /** Path of the markdown source relative to the docs dir, e.g. `servers/tools.md`. */
+    sourcePath: string;
+    /** Absolute URL of the markdown rendition. */
+    mdUrl: string;
+}
+
+interface Section {
+    title: string;
+    pages: Page[];
+}
+
+function toPage(site: string, title: string, route: string): Page {
+    const sourcePath = route === '/' ? 'index.md' : route.endsWith('/') ? `${route.slice(1)}index.md` : `${route.slice(1)}.md`;
+    return { title, sourcePath, mdUrl: `${site}/${sourcePath}` };
+}
+
+/** Flatten the sidebar into ordered sections, preserving sidebar order exactly. */
+function sections(site: string): Section[] {
+    const out: Section[] = [{ title: 'Overview', pages: [toPage(site, 'MCP TypeScript SDK', '/')] }];
+    for (const entry of guideSidebar as (DefaultTheme.SidebarItem & { items?: DefaultTheme.SidebarItem[] })[]) {
+        if (entry.items) {
+            out.push({ title: entry.text!, pages: entry.items.map(i => toPage(site, i.text!, i.link!)) });
+        } else {
+            out.push({ title: entry.text!, pages: [toPage(site, entry.text!, entry.link!)] });
+        }
+    }
+    return out;
+}
+
+/** Read a `description:` frontmatter value, if present. */
+function frontmatterDescription(markdown: string): string | undefined {
+    if (!markdown.startsWith('---\n')) return undefined;
+    const end = markdown.indexOf('\n---\n', 4);
+    if (end === -1) return undefined;
+    const match = /^description:\s*(.+)$/m.exec(markdown.slice(4, end));
+    return match?.[1].trim().replace(/^(['"])(.*)\1$/, '$2');
+}
+
+/** Strip `--- ... ---` frontmatter. */
+function stripFrontmatter(markdown: string): string {
+    if (!markdown.startsWith('---\n')) return markdown;
+    const end = markdown.indexOf('\n---\n', 4);
+    return end === -1 ? markdown : markdown.slice(end + 5).replace(/^\n+/, '');
+}
+
+/** Drop the `source="…"` wiring attribute from fence info lines. */
+function stripFenceAttributes(markdown: string): string {
+    return markdown.replace(/^```(\w+)\s+source="[^"]*"\s*$/gm, '```$1');
+}
+
+/**
+ * Absolutize every link for a page living at `pageDir` (docs-relative, '' for
+ * the root). Relative `.md` links stay `.md` so they resolve to the markdown
+ * renditions; `/specification/…` goes to modelcontextprotocol.io, mirroring
+ * the render-time rewrite in config.mts.
+ */
+function absolutizeLinks(markdown: string, pageDir: string, site: string, sourcePath: string): string {
+    // Runs over the raw markdown, code fences included — fine while no code
+    // sample contains a relative markdown link (none do; a false rewrite would
+    // show up in review of the rendition).
+    return markdown.replace(/\]\(([^)\s]+)\)/g, (match, target: string) => {
+        if (/^(https?:|mailto:|#)/.test(target)) return match;
+        if (target.startsWith('/specification/')) return `](https://modelcontextprotocol.io${target})`;
+        if (target.startsWith('/')) return `](${site}${target})`;
+        const hashIndex = target.indexOf('#');
+        const path = hashIndex === -1 ? target : target.slice(0, hashIndex);
+        const hash = hashIndex === -1 ? '' : target.slice(hashIndex);
+        let resolved = posix.normalize(posix.join(pageDir, path));
+        if (resolved.startsWith('..')) {
+            throw new Error(`${sourcePath}: relative link escapes the docs root: ${target} — use the site URL or a GitHub URL`);
+        }
+        if (resolved.startsWith('api/')) {
+            // The generated API reference has no markdown renditions — link its HTML.
+            resolved = resolved.replace(/\.md$/, '.html');
+        }
+        return `](${site}/${resolved}${hash})`;
+    });
+}
+
+function renderPage(docsDir: string, page: Page, site: string): { markdown: string; description?: string } {
+    const raw = readFileSync(join(docsDir, page.sourcePath), 'utf8');
+    const pageDir = posix.dirname(page.sourcePath);
+    return {
+        markdown: absolutizeLinks(stripFenceAttributes(stripFrontmatter(raw)), pageDir === '.' ? '' : pageDir, site, page.sourcePath),
+        description: frontmatterDescription(raw)
+    };
+}
+
+/** First prose sentence after the H1, markdown stripped, for the llms.txt index line. */
+function describe(rendered: string): string {
+    const lines = rendered.split('\n');
+    let inFence = false;
+    let inContainer = false;
+    let past = false;
+    const paragraph: string[] = [];
+    for (const line of lines) {
+        if (line.startsWith('```')) {
+            inFence = !inFence;
+            continue;
+        }
+        if (inFence) continue;
+        if (line.startsWith(':::')) {
+            inContainer = line.trim() !== ':::';
+            continue;
+        }
+        if (inContainer) continue;
+        if (line.startsWith('# ')) {
+            past = true;
+            continue;
+        }
+        if (!past) continue;
+        if (line.trim() === '' || /^[#>|]|^[-*] /.test(line)) {
+            if (paragraph.length > 0) break;
+            continue;
+        }
+        paragraph.push(line.trim());
+    }
+    const plain = paragraph
+        .join(' ')
+        .replace(/\[([^\]]*)\]\([^)]*\)/g, '$1')
+        .replace(/[*`]/g, '')
+        .trim();
+    const sentence = /^(.*?[.!?])(\s|$)/.exec(plain);
+    const blurb = sentence ? sentence[1] : plain;
+    return blurb.length > 220 ? `${blurb.slice(0, 217).replace(/\s+\S*$/, '')}…` : blurb;
+}
+
+/**
+ * Generate llms.txt, llms-full.txt, and the per-page markdown renditions into
+ * `outDir`. `site` is the absolute site URL without a trailing slash
+ * (origin + base), owned by config.mts.
+ */
+export function generateLlmsArtifacts(docsDir: string, outDir: string, site: string): void {
+    const groups = sections(site);
+    const rendered = new Map<string, { markdown: string; blurb: string }>();
+
+    for (const section of groups) {
+        for (const page of section.pages) {
+            const { markdown, description } = renderPage(docsDir, page, site);
+            rendered.set(page.sourcePath, { markdown, blurb: description ?? describe(markdown) });
+            const outPath = join(outDir, page.sourcePath);
+            mkdirSync(dirname(outPath), { recursive: true });
+            writeFileSync(outPath, markdown);
+        }
+    }
+
+    const header = [
+        '# MCP TypeScript SDK',
+        '',
+        '> The official TypeScript SDK for the Model Context Protocol (MCP): build MCP servers and clients on Node.js, Bun, Deno, and Workers. This is the v2 beta documentation, tracking the 2026-07-28 spec revision.',
+        '',
+        'Every page below is also served as plain markdown at its `.md` URL — fetch any page directly.',
+        ''
+    ];
+
+    const index = [...header];
+    for (const section of groups) {
+        index.push(`## ${section.title}`, '');
+        for (const page of section.pages) {
+            const blurb = rendered.get(page.sourcePath)!.blurb;
+            index.push(`- [${page.title}](${page.mdUrl})${blurb ? `: ${blurb}` : ''}`);
+        }
+        index.push('');
+    }
+    index.push(
+        '## Optional',
+        '',
+        `- [llms-full.txt](${site}/llms-full.txt): every page above concatenated into one file`,
+        `- [API reference](${site}/api/): generated per-package API reference`,
+        '- [MCP specification](https://modelcontextprotocol.io/specification/latest)',
+        '- [v1 documentation](https://ts.sdk.modelcontextprotocol.io/)',
+        ''
+    );
+    writeFileSync(join(outDir, 'llms.txt'), index.join('\n'));
+
+    // A separator no page body contains ('---' appears in the guides as a
+    // thematic break, so it cannot delimit pages unambiguously).
+    const separator = '='.repeat(80);
+    const full = [...header];
+    for (const section of groups) {
+        for (const page of section.pages) {
+            full.push(separator, `Source: ${page.mdUrl}`, separator, '', rendered.get(page.sourcePath)!.markdown.trimEnd(), '');
+        }
+    }
+    writeFileSync(join(outDir, 'llms-full.txt'), full.join('\n'));
+
+    console.log(`[docs] llms.txt, llms-full.txt, and ${rendered.size} markdown renditions written`);
+}
diff --git a/docs/.vitepress/nav.ts b/docs/.vitepress/nav.ts
new file mode 100644
index 0000000000..02ab4d2ff6
--- /dev/null
+++ b/docs/.vitepress/nav.ts
@@ -0,0 +1,85 @@
+import type { DefaultTheme } from 'vitepress';
+
+/**
+ * The guide sidebar: every hand-written page, in reading order. Shared by the
+ * site config (which appends the generated API Reference group) and the
+ * llms.txt generator (which mirrors these groups and this order).
+ */
+export const guideSidebar: DefaultTheme.SidebarItem[] = [
+    {
+        text: 'Get started',
+        items: [
+            { text: 'Build a server', link: '/get-started/first-server' },
+            { text: 'Plug into a real host', link: '/get-started/real-host' },
+            { text: 'Build a client', link: '/get-started/first-client' },
+            { text: 'Packages', link: '/get-started/packages' },
+            { text: 'Examples', link: '/get-started/examples' }
+        ]
+    },
+    {
+        text: 'Servers',
+        items: [
+            { text: 'Tools', link: '/servers/tools' },
+            { text: 'Resources', link: '/servers/resources' },
+            { text: 'Prompts', link: '/servers/prompts' },
+            { text: 'Completion', link: '/servers/completion' },
+            { text: 'Logging, progress, cancellation', link: '/servers/logging-progress-cancellation' },
+            { text: 'Elicitation', link: '/servers/elicitation' },
+            { text: 'Sampling (sunset)', link: '/servers/sampling' },
+            { text: 'Input required', link: '/servers/input-required' },
+            { text: 'Notifications', link: '/servers/notifications' },
+            { text: 'Errors', link: '/servers/errors' }
+        ]
+    },
+    {
+        text: 'Serving',
+        items: [
+            { text: 'stdio', link: '/serving/stdio' },
+            { text: 'HTTP', link: '/serving/http' },
+            { text: 'Express', link: '/serving/express' },
+            { text: 'Hono', link: '/serving/hono' },
+            { text: 'Fastify', link: '/serving/fastify' },
+            { text: 'Web-standard runtimes', link: '/serving/web-standard' },
+            { text: 'Sessions, state, scaling', link: '/serving/sessions-state-scaling' },
+            { text: 'Authorization', link: '/serving/authorization' },
+            { text: 'Legacy clients', link: '/serving/legacy-clients' }
+        ]
+    },
+    {
+        text: 'Clients',
+        items: [
+            { text: 'Connect', link: '/clients/connect' },
+            { text: 'Calling', link: '/clients/calling' },
+            { text: 'Handle server requests', link: '/clients/server-requests' },
+            { text: 'Roots (sunset)', link: '/clients/roots' },
+            { text: 'Subscriptions', link: '/clients/subscriptions' },
+            { text: 'OAuth', link: '/clients/oauth' },
+            { text: 'Machine auth', link: '/clients/machine-auth' },
+            { text: 'Middleware', link: '/clients/middleware' },
+            { text: 'Caching', link: '/clients/caching' }
+        ]
+    },
+    { text: 'Protocol versions', link: '/protocol-versions' },
+    {
+        text: 'Advanced',
+        collapsed: true,
+        items: [
+            { text: 'Low-level server', link: '/advanced/low-level-server' },
+            { text: 'Custom methods', link: '/advanced/custom-methods' },
+            { text: 'Schema libraries', link: '/advanced/schema-libraries' },
+            { text: 'Custom transports', link: '/advanced/custom-transports' },
+            { text: 'Wire schemas', link: '/advanced/wire-schemas' },
+            { text: 'Gateway', link: '/advanced/gateway' }
+        ]
+    },
+    { text: 'Testing', link: '/testing' },
+    { text: 'Troubleshooting', link: '/troubleshooting' },
+    {
+        text: 'Migration',
+        items: [
+            { text: 'Overview', link: '/migration/' },
+            { text: 'Upgrade to v2', link: '/migration/upgrade-to-v2' },
+            { text: '2026-07-28 protocol support', link: '/migration/support-2026-07-28' }
+        ]
+    }
+];
diff --git a/docs/clients/machine-auth.md b/docs/clients/machine-auth.md
index 34d24f8450..1b3c6614bb 100644
--- a/docs/clients/machine-auth.md
+++ b/docs/clients/machine-auth.md
@@ -1,5 +1,6 @@
 ---
 shape: how-to
+description: 'Authenticate a client with no user present: client credentials, private-key JWT, and cross-app access.'
 ---
 # Authenticate without a user
 
diff --git a/docs/clients/oauth.md b/docs/clients/oauth.md
index ed972919e1..f30dcd9258 100644
--- a/docs/clients/oauth.md
+++ b/docs/clients/oauth.md
@@ -1,5 +1,6 @@
 ---
 shape: how-to
+description: 'Sign an end user in from a client you build with the OAuth authorization-code flow.'
 ---
 # Authenticate a user with OAuth
 
diff --git a/docs/migration/upgrade-to-v2.md b/docs/migration/upgrade-to-v2.md
index 08c6a3e953..4749f1a8d1 100644
--- a/docs/migration/upgrade-to-v2.md
+++ b/docs/migration/upgrade-to-v2.md
@@ -202,7 +202,7 @@ per-member declarations; per-member is recommended, since the v2 package split m
 actual needs explicit. To answer "which packages does this member need" directly, run
 the codemod against that member's directory with `--dry-run`: the manifest summary is
 computed from that member's own imports. (The authoritative import-path routing lives
-in the codemod's [mapping file](../../packages/codemod/src/migrations/v1-to-v2/mappings/importMap.ts).)
+in the codemod's [mapping file](https://github.com/modelcontextprotocol/typescript-sdk/blob/main/packages/codemod/src/migrations/v1-to-v2/mappings/importMap.ts).)
 
 The framework adapter packages declare their framework as a **peer dependency**
 (`express`, `hono`, `fastify`); v1 shipped them as direct deps. The codemod adds the
diff --git a/docs/serving/authorization.md b/docs/serving/authorization.md
index a6163e197f..97f76d1aba 100644
--- a/docs/serving/authorization.md
+++ b/docs/serving/authorization.md
@@ -1,5 +1,6 @@
 ---
 shape: how-to
+description: 'Require a bearer token on a server you run: verification, protected-resource metadata, and per-tool scopes.'
 ---
 # Require authorization
 
diff --git a/packages/codemod/src/bin/batchTest.ts b/packages/codemod/src/bin/batchTest.ts
index 8c71bf7164..1a6802bc86 100644
--- a/packages/codemod/src/bin/batchTest.ts
+++ b/packages/codemod/src/bin/batchTest.ts
@@ -157,19 +157,30 @@ function detectPm(repoRoot: string): string {
     return 'npm';
 }
 
-function installCommand(pm: string): string {
+export function installCommand(pm: string, opts: { hasOwnPnpmWorkspace: boolean; packageDirs: string[] }): string {
     if (pm !== 'pnpm') return `${pm} install --ignore-scripts`;
-    // pnpm walks up to find a workspace; clones live inside this SDK's pnpm workspace, so a plain
-    // `pnpm install` targets the OUTER workspace and never populates the clone's node_modules — every
-    // downstream check (tsc base config, tsup, vitest) then fails identically at baseline and post,
-    // masking real codemod signal.
-    //   --ignore-workspace:    treat the clone as a standalone project (not part of the SDK workspace).
-    //   --no-frozen-lockfile:  the codemod rewrites package.json to swap v1 → v2 deps, so the lockfile
-    //                          must be allowed to change. CI=true (set in shell()) otherwise defaults
-    //                          pnpm to a frozen lockfile and the post-codemod reinstall silently skips
-    //                          the new v2 deps, leaving the clone on v1.
-    // npm/yarn/bun key off a `workspaces` field in package.json (absent at this repo root), so they
-    // need no equivalent flags.
+    // --no-frozen-lockfile: the codemod rewrites package.json to swap v1 → v2 deps, so the lockfile must
+    //   be allowed to change. CI=true (set in shell()) otherwise defaults pnpm to a frozen lockfile and the
+    //   post-codemod reinstall silently skips the new v2 deps, leaving the clone on v1.
+    if (opts.hasOwnPnpmWorkspace) {
+        // The clone is its OWN pnpm workspace — pnpm-workspace.yaml defines catalog:/workspace: deps
+        // (e.g. mastra). `--ignore-workspace` would discard that file and pnpm would fail to resolve them
+        // (ERR_PNPM_CATALOG_ENTRY_NOT_FOUND_FOR_SPEC; unresolved workspace: links → repo skipped). We don't
+        // need it: the SDK workspace excludes the clones (`!packages/codemod/batch-test/**`) and pnpm uses
+        // the clone's own pnpm-workspace.yaml as the nearest root. Scope the install to the target packages
+        // and their dependencies (`{./<dir>}...`) so a monorepo target installs only what the checks need
+        // (e.g. 2 of mastra's 161 projects) instead of the whole tree. The braces are load-bearing: pnpm
+        // silently ignores the trailing `...` on a bare `./<dir>...` path selector (installing the package
+        // without its workspace deps); the `{./<dir>}...` form honors it.
+        const filters = opts.packageDirs
+            .filter(dir => dir !== '.')
+            .map(dir => `--filter ${JSON.stringify(`{./${dir}}...`)}`)
+            .join(' ');
+        return `pnpm install --ignore-scripts --no-frozen-lockfile${filters ? ` ${filters}` : ''}`;
+    }
+    // Single-package clone with no workspace of its own: pnpm would walk up to the (clone-excluding) SDK
+    // workspace and never populate the clone's node_modules. `--ignore-workspace` treats it as standalone.
+    // npm/yarn/bun key off a `workspaces` field in package.json (absent at this repo root).
     return 'pnpm install --ignore-scripts --ignore-workspace --no-frozen-lockfile';
 }
 
@@ -643,18 +654,23 @@ function main(): void {
         const pm = detectPm(clonePath);
         console.log(`  Package manager: ${pm}`);
 
-        // Step 3: Install
+        // Process packages
+        const packages: PackageEntry[] = entry.packages ?? [{ dir: '.', sourceDir: 'src' }];
+        const repoPkgResults: PackageReport[] = [];
+
+        // Step 3: Install. A clone that is its own pnpm workspace (catalog:/workspace: deps) must keep its
+        // pnpm-workspace.yaml — see installCommand. Computed once and reused for the post-codemod reinstall.
+        const installCmd = installCommand(pm, {
+            hasOwnPnpmWorkspace: existsSync(path.join(clonePath, 'pnpm-workspace.yaml')),
+            packageDirs: packages.map(p => p.dir)
+        });
         console.log('  Installing dependencies...');
-        const installResult = shell(installCommand(pm), clonePath);
+        const installResult = shell(installCmd, clonePath);
         if (installResult.exitCode !== 0) {
             console.log(`  ERROR: install failed, skipping\n  ${installResult.stderr.split('\n')[0]}`);
             continue;
         }
 
-        // Process packages
-        const packages: PackageEntry[] = entry.packages ?? [{ dir: '.', sourceDir: 'src' }];
-        const repoPkgResults: PackageReport[] = [];
-
         for (const pkg of packages) {
             const sourceDir = pkg.sourceDir ?? 'src';
             const fullPkgDir = path.join(clonePath, pkg.dir);
@@ -697,7 +713,7 @@ function main(): void {
                 if (rewrites > 0) console.log(`    Pinned ${rewrites} deps to resolved published versions`);
             }
             console.log('    Re-installing dependencies...');
-            shell(installCommand(pm), clonePath);
+            shell(installCmd, clonePath);
 
             // Step 7: Post-codemod checks
             console.log('    Running post-codemod checks...');
diff --git a/packages/codemod/src/generated/versions.ts b/packages/codemod/src/generated/versions.ts
index 196a367508..a82d986db8 100644
--- a/packages/codemod/src/generated/versions.ts
+++ b/packages/codemod/src/generated/versions.ts
@@ -1,9 +1,9 @@
 // AUTO-GENERATED — do not edit. Run `pnpm run generate:versions` to regenerate.
 export const V2_PACKAGE_VERSIONS: Record<string, string> = {
-    '@modelcontextprotocol/client': '^2.0.0-alpha.3',
-    '@modelcontextprotocol/server': '^2.0.0-alpha.3',
-    '@modelcontextprotocol/node': '^2.0.0-alpha.3',
-    '@modelcontextprotocol/express': '^2.0.0-alpha.3',
-    '@modelcontextprotocol/server-legacy': '^2.0.0-alpha.3',
-    '@modelcontextprotocol/core': '^2.0.0-alpha.1'
+    '@modelcontextprotocol/client': '^2.0.0-beta.1',
+    '@modelcontextprotocol/server': '^2.0.0-beta.1',
+    '@modelcontextprotocol/node': '^2.0.0-beta.1',
+    '@modelcontextprotocol/express': '^2.0.0-beta.1',
+    '@modelcontextprotocol/server-legacy': '^2.0.0-beta.1',
+    '@modelcontextprotocol/core': '^2.0.0-beta.1'
 };
diff --git a/packages/codemod/src/migrations/v1-to-v2/transforms/contextTypes.ts b/packages/codemod/src/migrations/v1-to-v2/transforms/contextTypes.ts
index dd8abbd137..f0f733ba32 100644
--- a/packages/codemod/src/migrations/v1-to-v2/transforms/contextTypes.ts
+++ b/packages/codemod/src/migrations/v1-to-v2/transforms/contextTypes.ts
@@ -1,4 +1,4 @@
-import type { SourceFile } from 'ts-morph';
+import type { ObjectLiteralExpression, SourceFile } from 'ts-morph';
 import { Node, SyntaxKind } from 'ts-morph';
 
 import type { Diagnostic, Transform, TransformContext, TransformResult } from '../../../types';
@@ -9,8 +9,33 @@ import { CONTEXT_PROPERTY_MAP, CTX_PARAM_NAME, EXTRA_PARAM_NAME } from '../mappi
 
 const CONTEXT_LIKE_KEYS = new Set(CONTEXT_PROPERTY_MAP.map(mapping => mapping.from.slice(1)));
 
+/**
+ * v1 context keys distinctive enough that a single one on an object literal is a strong
+ * signal it's a hand-built handler-context mock (vs. generic keys like `signal`/`sessionId`/
+ * `requestId` — a bare correlation-ID literal such as `logger.info(msg, { requestId })` is
+ * not a context mock — which appear on unrelated objects and only count in aggregate).
+ */
+const DISTINCTIVE_CONTEXT_KEYS = new Set([
+    'sendRequest',
+    'sendNotification',
+    'requestInfo',
+    'authInfo',
+    'closeSSEStream',
+    'closeStandaloneSSEStream'
+]);
+
+/** A literal already carrying one of these is in the v2 nested shape — not a stale v1 mock. */
+const V2_SHAPE_KEYS = new Set(['mcpReq', 'http', 'task']);
+
 const HANDLER_METHODS = new Set(['setRequestHandler', 'setNotificationHandler']);
 
+/**
+ * Transport ingestion methods whose second argument is a flat `MessageExtraInfo`
+ * (authInfo/request/closeSSEStream/… stay top-level in v2), NOT a handler context —
+ * so a literal handed to them must never get handler-context reshape guidance.
+ */
+const TRANSPORT_MESSAGE_METHODS = new Set(['onmessage', 'handleMessage']);
+
 const REGISTER_METHODS = new Set(['registerTool', 'registerPrompt', 'registerResource', 'tool', 'prompt', 'resource']);
 
 /**
@@ -303,6 +328,7 @@ export const contextTypesTransform: Transform = {
 
         changesCount += processFallbackHandlerAssignments(sourceFile, diagnostics);
         changesCount += remapAnnotatedContextParams(sourceFile, diagnostics);
+        flagV1MockContextLiterals(sourceFile, diagnostics);
 
         return { changesCount, diagnostics };
     }
@@ -329,6 +355,108 @@ function processFallbackHandlerAssignments(sourceFile: SourceFile, diagnostics:
     return changes;
 }
 
+/**
+ * Render a v1 context key as a reshape hint, e.g. `sendRequest` → `mcpReq.send`. Returns
+ * undefined for `sessionId` (a no-op — it stays top-level in v2) and for non-context keys.
+ */
+function contextKeyReshapeHint(key: string): string | undefined {
+    const mapping = CONTEXT_PROPERTY_MAP.find(m => m.from === '.' + key);
+    if (mapping === undefined || mapping.from === mapping.to) return undefined;
+    // Render the target as a plain object path: '.http?.authInfo' → 'http.authInfo'.
+    return `${key} → ${mapping.to.replace(/^\./, '').replaceAll('?', '')}`;
+}
+
+/**
+ * Flag hand-built mocks of the handler context (common in tests). The call-site scan above
+ * only reshapes `extra.X` inside handler definitions it can anchor on (registerTool,
+ * setRequestHandler, fallback handlers, annotated params). A test hands its mock to a bare
+ * `handler(args, mockCtx)` invocation, so the object literal is never reached and keeps the
+ * flat v1 shape — at runtime the migrated handler reads `ctx.mcpReq.send` / `.id` / … against
+ * it and throws "Cannot read properties of undefined (reading 'send')". Advisory only: an
+ * untyped literal that merely shares a key name might not be a context mock, so never rewrite.
+ */
+function flagV1MockContextLiterals(sourceFile: SourceFile, diagnostics: Diagnostic[]): void {
+    for (const obj of sourceFile.getDescendantsOfKind(SyntaxKind.ObjectLiteralExpression)) {
+        // Only literals in a mock-context position: a call argument or a variable initializer.
+        // Covers both `handler({}, { sendRequest: fn })` and `const extra = { … }; handler(a, extra)`.
+        // Unwrap casts/parens first so typed mocks — `{ … } as unknown as RequestHandlerExtra`,
+        // `({ … })`, `{ … } satisfies X` — are anchored by what encloses the cast, not the
+        // AsExpression that directly wraps the literal.
+        let expr: Node = obj;
+        let parent = expr.getParent();
+        while (
+            parent !== undefined &&
+            (Node.isAsExpression(parent) || Node.isSatisfiesExpression(parent) || Node.isParenthesizedExpression(parent))
+        ) {
+            expr = parent;
+            parent = parent.getParent();
+        }
+        const isCallArg = parent !== undefined && Node.isCallExpression(parent) && parent.getArguments().includes(expr);
+        const isVarInit = parent !== undefined && Node.isVariableDeclaration(parent) && parent.getInitializer() === expr;
+        if (!isCallArg && !isVarInit) continue;
+
+        // A literal handed to a transport ingestion method (`transport.onmessage(msg, { … })`,
+        // `transport.handleMessage(msg, { … })`) is a flat MessageExtraInfo, not a handler-context
+        // mock — reshaping its authInfo/request/closeSSEStream/… under http/mcpReq would be wrong.
+        if (isCallArg && Node.isCallExpression(parent)) {
+            const callee = parent.getExpression();
+            if (Node.isPropertyAccessExpression(callee) && TRANSPORT_MESSAGE_METHODS.has(callee.getName())) continue;
+        }
+
+        // The codemod's OWN output: an options object inside a just-rewritten handler whose values
+        // now read `ctx.mcpReq.*` / `ctx.http.*`. The keys keep their v1 names — so V2_SHAPE_KEYS
+        // below, which only inspects key names, won't catch it — but the values are already v2, not
+        // a stale mock. Flagging it would insert a comment above code the codemod itself produced.
+        if (readsFromMigratedContext(obj)) continue;
+
+        // Collect named property keys (skip spreads and computed names).
+        const keys: string[] = [];
+        for (const prop of obj.getProperties()) {
+            if (!Node.isPropertyAssignment(prop) && !Node.isShorthandPropertyAssignment(prop) && !Node.isMethodDeclaration(prop)) continue;
+            const nameNode = prop.getNameNode();
+            if (Node.isIdentifier(nameNode)) keys.push(nameNode.getText());
+            else if (Node.isStringLiteral(nameNode)) keys.push(nameNode.getLiteralText());
+        }
+        if (keys.some(key => V2_SHAPE_KEYS.has(key))) continue; // already v2-shaped
+
+        const contextKeys = keys.filter(key => CONTEXT_LIKE_KEYS.has(key));
+        const hasDistinctive = contextKeys.some(key => DISTINCTIVE_CONTEXT_KEYS.has(key));
+        if (!hasDistinctive && contextKeys.length < 2) continue;
+
+        const reshapes = contextKeys.map(key => contextKeyReshapeHint(key)).filter((hint): hint is string => hint !== undefined);
+        const sessionNote = contextKeys.includes('sessionId') ? '; sessionId stays top-level' : '';
+        diagnostics.push({
+            ...actionRequired(
+                sourceFile.getFilePath(),
+                obj,
+                `This object looks like a v1 handler-context mock (${contextKeys.join(', ')}). v2 nests the context — ` +
+                    `reshape it (${reshapes.join('; ')}${sessionNote}), e.g. { sendRequest: fn } → { mcpReq: { send: fn } }. ` +
+                    `Passed as-is to a migrated handler that reads ctx.mcpReq.*, the v1 shape throws ` +
+                    `"Cannot read properties of undefined".`
+            ),
+            advisoryOnly: true
+        });
+    }
+}
+
+/**
+ * True when any property value already reads from the v2-nested context — a `.mcpReq` or `.http`
+ * property access (e.g. `ctx.mcpReq.signal`, `ctx.http?.authInfo`). Such a literal is migrated
+ * output, not a hand-built v1 mock: a real v1 mock supplies raw values (`fn`, `ac.signal`, a
+ * literal), never the nested v2 shape the codemod itself just wrote.
+ */
+function readsFromMigratedContext(obj: ObjectLiteralExpression): boolean {
+    for (const prop of obj.getProperties()) {
+        if (!Node.isPropertyAssignment(prop)) continue;
+        const init = prop.getInitializer();
+        if (init === undefined) continue;
+        const accesses = init.getDescendantsOfKind(SyntaxKind.PropertyAccessExpression);
+        if (Node.isPropertyAccessExpression(init)) accesses.push(init);
+        if (accesses.some(access => access.getName() === 'mcpReq' || access.getName() === 'http')) return true;
+    }
+    return false;
+}
+
 const CONTEXT_TYPE_NAMES = new Set(['RequestHandlerExtra', 'ServerContext', 'ClientContext']);
 /**
  * Split a type's text on top-level `|` only (angle brackets tracked). Returns
diff --git a/packages/codemod/src/migrations/v1-to-v2/transforms/handlerRegistration.ts b/packages/codemod/src/migrations/v1-to-v2/transforms/handlerRegistration.ts
index 1ecfa00ce8..9c0ff40af7 100644
--- a/packages/codemod/src/migrations/v1-to-v2/transforms/handlerRegistration.ts
+++ b/packages/codemod/src/migrations/v1-to-v2/transforms/handlerRegistration.ts
@@ -173,6 +173,54 @@ export const handlerRegistrationTransform: Transform = {
             removeUnusedImport(sourceFile, schemaName, true);
         }
 
+        // Flag surviving registration-schema references. A method-mapped *RequestSchema/*NotificationSchema
+        // whose import survived the conversion above, used as a VALUE (a call argument or an `===`/`!==`
+        // operand), is almost always a stale v1 registration assertion/lookup — in v2 the registration key is
+        // the method string, not the schema. Advisory, not rewritten: the same constant is still valid for
+        // `.parse()` etc., so we flag rather than risk breaking a legitimate schema use.
+        //
+        // Gate on a registration MOCK/lookup, not on any setRequestHandler access. A file that only *calls*
+        // setRequestHandler/setNotificationHandler (real registrations, which the pass above rewrites) tells us
+        // nothing about its other schema references — those may be plain schema uses (`validateSchema(S)`,
+        // `zodToJsonSchema(S)`, `ajv.compile(S)`). Only a NON-call reference — `inner.setRequestHandler.mock`,
+        // `expect(x.setRequestHandler)…`, a comparison operand — signals the file makes registration
+        // assertions, where a surviving schema key is likely stale.
+        const usesRegistrationMock = sourceFile.getDescendantsOfKind(SyntaxKind.PropertyAccessExpression).some(pa => {
+            if (pa.getName() !== 'setRequestHandler' && pa.getName() !== 'setNotificationHandler') return false;
+            const paParent = pa.getParent();
+            // Exclude real registration calls `x.setRequestHandler(…)`, where pa is the callee.
+            return !(Node.isCallExpression(paParent) && paParent.getExpression() === pa);
+        });
+        if (usesRegistrationMock) {
+            const flagged = new Set<string>();
+            for (const id of sourceFile.getDescendantsOfKind(SyntaxKind.Identifier)) {
+                const local = id.getText();
+                if (flagged.has(local)) continue;
+                const original = resolveOriginalImportName(sourceFile, local) ?? local;
+                const method = ALL_SCHEMA_TO_METHOD[original];
+                if (method === undefined || !isImportedFromMcp(sourceFile, local)) continue;
+                const parent = id.getParent();
+                if (parent === undefined) continue;
+                const isCallArg = Node.isCallExpression(parent) && parent.getArguments().includes(id);
+                const isComparand =
+                    Node.isBinaryExpression(parent) &&
+                    ['===', '!==', '==', '!='].includes(parent.getOperatorToken().getText()) &&
+                    (parent.getLeft() === id || parent.getRight() === id);
+                if (!isCallArg && !isComparand) continue;
+                flagged.add(local);
+                diagnostics.push({
+                    ...actionRequired(
+                        sourceFile.getFilePath(),
+                        id,
+                        `${local} is no longer the setRequestHandler/setNotificationHandler key in v2 — handlers ` +
+                            `register by the method string '${method}'. Update registration assertions/lookups ` +
+                            `(e.g. against a setRequestHandler mock) to compare against '${method}'.`
+                    ),
+                    advisoryOnly: true
+                });
+            }
+        }
+
         return { changesCount, diagnostics };
     }
 };
diff --git a/packages/codemod/test/batchTest.test.ts b/packages/codemod/test/batchTest.test.ts
index 41ea0e9c61..2d470f027a 100644
--- a/packages/codemod/test/batchTest.test.ts
+++ b/packages/codemod/test/batchTest.test.ts
@@ -3,7 +3,7 @@ import { tmpdir } from 'node:os';
 import path from 'node:path';
 import { describe, it, expect, vi, afterEach } from 'vitest';
 
-import { parseArgs, parseCodemodCliOutput, runCodemod } from '../src/bin/batchTest';
+import { parseArgs, parseCodemodCliOutput, runCodemod, installCommand } from '../src/bin/batchTest';
 import { computeResultsDirName, type ResolvedConfig } from '../src/bin/batchTest';
 import { parseNpmViewVersion, rewriteToPublishedVersion, cleanSubprocessEnv } from '../src/bin/batchTest';
 import { getMigration } from '../src/migrations/index';
@@ -12,6 +12,35 @@ afterEach(() => {
     vi.restoreAllMocks();
 });
 
+describe('installCommand', () => {
+    it('uses plain --ignore-scripts for non-pnpm managers', () => {
+        expect(installCommand('npm', { hasOwnPnpmWorkspace: false, packageDirs: ['.'] })).toBe('npm install --ignore-scripts');
+        expect(installCommand('yarn', { hasOwnPnpmWorkspace: true, packageDirs: ['packages/a'] })).toBe('yarn install --ignore-scripts');
+    });
+
+    it('isolates a pnpm clone with no workspace of its own via --ignore-workspace', () => {
+        expect(installCommand('pnpm', { hasOwnPnpmWorkspace: false, packageDirs: ['.'] })).toBe(
+            'pnpm install --ignore-scripts --ignore-workspace --no-frozen-lockfile'
+        );
+    });
+
+    it('respects a pnpm clone that is its own workspace and scopes the install to the target packages', () => {
+        const cmd = installCommand('pnpm', { hasOwnPnpmWorkspace: true, packageDirs: ['packages/core', 'packages/mcp'] });
+        expect(cmd).not.toContain('--ignore-workspace');
+        // braces required: pnpm ignores the `...` on a bare `./dir...` selector (drops workspace deps);
+        // `{./dir}...` includes them.
+        expect(cmd).toBe(
+            'pnpm install --ignore-scripts --no-frozen-lockfile --filter "{./packages/core}..." --filter "{./packages/mcp}..."'
+        );
+    });
+
+    it('installs the whole workspace (no --filter) when the only target is the clone root', () => {
+        expect(installCommand('pnpm', { hasOwnPnpmWorkspace: true, packageDirs: ['.'] })).toBe(
+            'pnpm install --ignore-scripts --no-frozen-lockfile'
+        );
+    });
+});
+
 describe('parseArgs', () => {
     it('defaults to local/local with latest codemod version and unset sdk version', () => {
         const opts = parseArgs([]);
diff --git a/packages/codemod/test/v1-to-v2/transforms/contextTypes.test.ts b/packages/codemod/test/v1-to-v2/transforms/contextTypes.test.ts
index 4b41562c1e..b530dc4b34 100644
--- a/packages/codemod/test/v1-to-v2/transforms/contextTypes.test.ts
+++ b/packages/codemod/test/v1-to-v2/transforms/contextTypes.test.ts
@@ -2,7 +2,7 @@ import { describe, it, expect } from 'vitest';
 import { Project } from 'ts-morph';
 
 import { contextTypesTransform } from '../../../src/migrations/v1-to-v2/transforms/contextTypes';
-import type { TransformContext } from '../../../src/types';
+import type { Diagnostic, TransformContext } from '../../../src/types';
 
 const ctx: TransformContext = { projectType: 'server' };
 
@@ -637,3 +637,121 @@ describe('fallback handler and annotated context params (B5, #152)', () => {
         expect(diag?.advisoryOnly).toBe(true);
     });
 });
+
+describe('v1 mock context literals in tests (test doubles)', () => {
+    function apply(code: string) {
+        const project = new Project({ useInMemoryFileSystem: true });
+        const sourceFile = project.createSourceFile('test.ts', code);
+        const result = contextTypesTransform.apply(sourceFile, { projectType: 'server' });
+        return { text: sourceFile.getFullText(), result };
+    }
+    const IMPORT = `import { McpServer } from '@modelcontextprotocol/server';\n`;
+    const findMockDiag = (diags: Diagnostic[]) => diags.find(d => d.message.includes('v1 handler-context mock'));
+
+    it('advises (without rewriting) on a v1 context mock passed inline as a call argument', () => {
+        const code = IMPORT + [`const r = await handler({}, { sendRequest: mockSendRequest });`, ''].join('\n');
+        const { text, result } = apply(code);
+        // Advisory only — the literal is left untouched.
+        expect(text).toContain('{ sendRequest: mockSendRequest }');
+        const diag = findMockDiag(result.diagnostics);
+        expect(diag).toBeDefined();
+        expect(diag?.advisoryOnly).toBe(true);
+        expect(diag?.message).toContain('sendRequest → mcpReq.send');
+    });
+
+    it('advises on a v1 context mock bound to a variable, and notes sessionId stays top-level', () => {
+        const code = IMPORT + [`const extra = { sessionId: 'session-1', sendRequest: fn };`, `await handler(args, extra);`, ''].join('\n');
+        const { result } = apply(code);
+        const diag = findMockDiag(result.diagnostics);
+        expect(diag).toBeDefined();
+        expect(diag?.advisoryOnly).toBe(true);
+        expect(diag?.message).toContain('sessionId stays top-level');
+    });
+
+    it('advises on the _meta/requestId progress-notification mock shape', () => {
+        const code = IMPORT + [`await handler({ duration: 1 }, { _meta: {}, requestId: 'test-123' });`, ''].join('\n');
+        const { result } = apply(code);
+        const diag = findMockDiag(result.diagnostics);
+        expect(diag).toBeDefined();
+        expect(diag?.message).toContain('requestId → mcpReq.id');
+    });
+
+    it('advises when two generic context keys appear together (no distinctive key)', () => {
+        const code = IMPORT + [`await handler(args, { signal: ac.signal, sessionId: 's' });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeDefined();
+    });
+
+    it('does not advise on an already-migrated v2 context mock', () => {
+        const code = IMPORT + [`await handler({}, { mcpReq: { send: fn } });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('does not advise on a non-context object literal', () => {
+        const code = IMPORT + [`const config = { title: 'x', description: 'y' };`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('does not advise on a lone generic key (needs a distinctive key or >=2 context keys)', () => {
+        const code = IMPORT + [`doThing({ signal: ac.signal });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('does not advise on a lone requestId (a bare correlation-ID literal, not a context mock)', () => {
+        const code = IMPORT + [`logger.info('handling lookup', { requestId: args.id });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('advises on a cast-wrapped inline mock (`{ … } as unknown as RequestHandlerExtra`)', () => {
+        const code = IMPORT + [`await handler(args, { sendRequest: fn } as unknown as RequestHandlerExtra);`, ''].join('\n');
+        const { result } = apply(code);
+        const diag = findMockDiag(result.diagnostics);
+        expect(diag).toBeDefined();
+        expect(diag?.advisoryOnly).toBe(true);
+    });
+
+    it('advises on a cast-wrapped variable mock (`const ctx = { … } as any`)', () => {
+        const code = IMPORT + [`const mockCtx = { requestId: 1, sendRequest: fn } as any;`, `await handler(args, mockCtx);`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeDefined();
+    });
+
+    it('does not advise on already-v2 values (an options object reading ctx.mcpReq / ctx.sessionId)', () => {
+        const code = IMPORT + [`doThing({ signal: ctx.mcpReq.signal, sessionId: ctx.sessionId });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it("does not re-flag the codemod's own migrated handler output", () => {
+        const code =
+            IMPORT +
+            [
+                `server.setRequestHandler('x', async (req, extra) => {`,
+                `    await loadData(req.uri, { signal: extra.signal, sessionId: extra.sessionId });`,
+                `    return {};`,
+                `});`,
+                ''
+            ].join('\n');
+        const { text, result } = apply(code);
+        // sanity: the handler body WAS migrated to the v2 nested shape …
+        expect(text).toContain('ctx.mcpReq.signal');
+        // … and the resulting options object is not mistaken for a stale v1 mock.
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('does not advise on a flat MessageExtraInfo literal passed to onmessage', () => {
+        const code = IMPORT + [`transport.onmessage(msg, { requestInfo: req, authInfo });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+
+    it('does not advise on a flat MessageExtraInfo literal passed to handleMessage', () => {
+        const code = IMPORT + [`await transport.handleMessage(msg, { authInfo, closeSSEStream: fn });`, ''].join('\n');
+        const { result } = apply(code);
+        expect(findMockDiag(result.diagnostics)).toBeUndefined();
+    });
+});
diff --git a/packages/codemod/test/v1-to-v2/transforms/handlerRegistration.test.ts b/packages/codemod/test/v1-to-v2/transforms/handlerRegistration.test.ts
index b29f1cefcb..6cf7f136d1 100644
--- a/packages/codemod/test/v1-to-v2/transforms/handlerRegistration.test.ts
+++ b/packages/codemod/test/v1-to-v2/transforms/handlerRegistration.test.ts
@@ -394,3 +394,72 @@ describe('variable-hop guard rails (B6 review)', () => {
         expect(result.diagnostics.some(d => d.message.includes('Custom method handler'))).toBe(true);
     });
 });
+
+describe('stale registration-schema references (analysis: mcp-servers/memory)', () => {
+    function applyWithDiagnostics(code: string) {
+        const project = new Project({ useInMemoryFileSystem: true });
+        const sourceFile = project.createSourceFile('test.ts', code);
+        const result = handlerRegistrationTransform.apply(sourceFile, { projectType: 'server' });
+        return { text: sourceFile.getFullText(), result };
+    }
+
+    it('flags a request schema used as a setRequestHandler-mock assertion arg with the method string', () => {
+        const code = [
+            `import { SubscribeRequestSchema } from '@modelcontextprotocol/sdk/types.js';`,
+            `const schemas = inner.setRequestHandler.mock.calls.map((c) => c[0]);`,
+            `expect(schemas).toContain(SubscribeRequestSchema);`,
+            ''
+        ].join('\n');
+        const { result } = applyWithDiagnostics(code);
+        const diag = result.diagnostics.find(
+            d => d.message.includes('SubscribeRequestSchema') && d.message.includes("'resources/subscribe'")
+        );
+        expect(diag).toBeDefined();
+    });
+
+    it('flags a schema passed to a registration-lookup helper', () => {
+        const code = [
+            `import { UnsubscribeRequestSchema } from '@modelcontextprotocol/sdk/types.js';`,
+            `const c = inner.setRequestHandler.mock.calls.find((x) => x[0] === s);`,
+            `handlerFor(inner, UnsubscribeRequestSchema);`,
+            ''
+        ].join('\n');
+        const { result } = applyWithDiagnostics(code);
+        expect(result.diagnostics.some(d => d.message.includes("'resources/unsubscribe'"))).toBe(true);
+    });
+
+    it('does NOT flag a request schema used as a schema (.parse) — property-access base', () => {
+        const code = [
+            `import { CallToolRequestSchema } from '@modelcontextprotocol/sdk/types.js';`,
+            `server.setRequestHandler(CallToolRequestSchema, async () => ({ content: [] }));`,
+            `const parsed = CallToolRequestSchema.parse(x);`,
+            ''
+        ].join('\n');
+        const { result } = applyWithDiagnostics(code);
+        expect(result.diagnostics.some(d => d.message.includes('no longer the setRequestHandler'))).toBe(false);
+    });
+
+    it('does NOT flag in a file that performs no handler registration', () => {
+        const code = [
+            `import { SubscribeRequestSchema } from '@modelcontextprotocol/sdk/types.js';`,
+            `someValidator(SubscribeRequestSchema);`,
+            ''
+        ].join('\n');
+        const { result } = applyWithDiagnostics(code);
+        expect(result.diagnostics.some(d => d.message.includes('no longer the setRequestHandler'))).toBe(false);
+    });
+
+    it('does NOT flag a schema consumed by a validator when setRequestHandler is only a real registration', () => {
+        // The file registers a handler for real (a call the pass rewrites); an unrelated schema-consuming
+        // call like validateSchema(S) / zodToJsonSchema(S) is not a stale registration key — only a
+        // setRequestHandler MOCK/lookup reference signals that surviving schema refs are stale.
+        const code = [
+            `import { CallToolRequestSchema, SubscribeRequestSchema } from '@modelcontextprotocol/sdk/types.js';`,
+            `server.setRequestHandler(CallToolRequestSchema, async () => ({ content: [] }));`,
+            `validateSchema(SubscribeRequestSchema);`,
+            ''
+        ].join('\n');
+        const { result } = applyWithDiagnostics(code);
+        expect(result.diagnostics.some(d => d.message.includes('no longer the setRequestHandler'))).toBe(false);
+    });
+});