diff --git a/.agents/PROJECT.md b/.agents/PROJECT.md
index 94bbed88..9f7057c2 100644
--- a/.agents/PROJECT.md
+++ b/.agents/PROJECT.md
@@ -214,6 +214,7 @@ The package README documents the `kb.yaml` configuration schema and merge semant
 **Root-level development (via `@williamthorsen/nmr`):**
 
 - `pnpm install` - Install all dependencies
+- `pnpm run bootstrap` - Build every package; required after install before the MCP server or CLI bins will run
 - `nmr check` - Run typecheck, format check, lint check, and tests
 - `nmr check:strict` - Strict checks including coverage and audit
 - `nmr ci` - Full CI pipeline (strict checks + build)
diff --git a/.config/wt.toml b/.config/wt.toml
index 916fc033..1b4a2750 100644
--- a/.config/wt.toml
+++ b/.config/wt.toml
@@ -3,4 +3,4 @@
 [post-create]
 direnv = "direnv allow"
 deps = "pnpm install"
-build = "nmr build"
+bootstrap = "pnpm run bootstrap"
diff --git a/.github/workflows/code-quality.yaml b/.github/workflows/code-quality.yaml
index e5bf20ea..2a964469 100644
--- a/.github/workflows/code-quality.yaml
+++ b/.github/workflows/code-quality.yaml
@@ -25,4 +25,4 @@ jobs:
   code-quality:
     uses: williamthorsen/.github/.github/workflows/code-quality-pnpm-workflow.yaml@v7
     with:
-      check-command: pnpm exec nmr build && pnpm exec nmr check:strict
+      check-command: pnpm exec nmr check:strict
diff --git a/README.md b/README.md
index 6b49658a..5c4aa6a5 100644
--- a/README.md
+++ b/README.md
@@ -10,5 +10,6 @@ See [`.agents/PROJECT.md`](.agents/PROJECT.md) for project structure, commands,
 
 ```bash
 pnpm install
-nmr check  # Run all checks (typecheck, format, lint, test)
+pnpm run bootstrap   # Build every package; required before running the MCP server or CLI bins
+pnpm exec nmr check  # Run all checks (typecheck, format, lint, test)
 ```
diff --git a/package.json b/package.json
index 01613896..683ae4a3 100644
--- a/package.json
+++ b/package.json
@@ -21,6 +21,7 @@
   "scripts": {
     "agents:install": "tsx packages/agents/src/cli.ts install",
     "agents:install-launchers": "bash packages/agents/scripts/install-launchers.sh",
+    "bootstrap": "nmr build",
     "ci:post": "pnpm --filter agents run test:sh",
     "prepare": "lefthook install"
   },
diff --git a/packages/agents/bin/codeassembly-agents.js b/packages/agents/bin/codeassembly-agents.js
index 02293471..92ea0c71 100755
--- a/packages/agents/bin/codeassembly-agents.js
+++ b/packages/agents/bin/codeassembly-agents.js
@@ -11,7 +11,7 @@ const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
 // module in the graph, so keying the build-first message off the error code would also
 // fire when the build is present and one of its imports is missing.
 if (!existsSync(entryPoint)) {
-  process.stderr.write('codeassembly-agents: build output not found — run `pnpm run build` first\n');
+  process.stderr.write('codeassembly-agents: build output not found — run `pnpm run bootstrap` first\n');
   process.exit(1);
 }
 
diff --git a/packages/kb/bin/kb.js b/packages/kb/bin/kb.js
index 2824bd3d..a9b49a07 100755
--- a/packages/kb/bin/kb.js
+++ b/packages/kb/bin/kb.js
@@ -11,7 +11,7 @@ const entryPoint = new URL('../dist/esm/cli/index.js', import.meta.url);
 // module in the graph, so keying the build-first message off the error code would also
 // fire when the build is present and one of its imports is missing.
 if (!existsSync(entryPoint)) {
-  process.stderr.write('kb: build output not found — run `pnpm run build` first\n');
+  process.stderr.write('kb: build output not found — run `pnpm run bootstrap` first\n');
   process.exit(1);
 }
 
diff --git a/packages/kb/package.json b/packages/kb/package.json
index 79454d5c..a65b64c8 100644
--- a/packages/kb/package.json
+++ b/packages/kb/package.json
@@ -76,8 +76,7 @@
     "!dist/esm/test-utils"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "dependencies": {
     "picomatch": "4.0.5",
diff --git a/packages/lifecycle/package.json b/packages/lifecycle/package.json
index fa25b811..f259134d 100644
--- a/packages/lifecycle/package.json
+++ b/packages/lifecycle/package.json
@@ -16,8 +16,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "devDependencies": {
     "esbuild": "0.28.1"
diff --git a/packages/mcp/bin/codeassembly-mcp.js b/packages/mcp/bin/codeassembly-mcp.js
index fd7e0a62..8abe44a0 100755
--- a/packages/mcp/bin/codeassembly-mcp.js
+++ b/packages/mcp/bin/codeassembly-mcp.js
@@ -11,7 +11,7 @@ const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
 // module in the graph, so keying the build-first message off the error code would also
 // fire when the build is present and one of its imports is missing.
 if (!existsSync(entryPoint)) {
-  process.stderr.write('codeassembly-mcp: build output not found — run `pnpm run build` first\n');
+  process.stderr.write('codeassembly-mcp: build output not found — run `pnpm run bootstrap` first\n');
   process.exit(1);
 }
 
diff --git a/packages/mcp/package.json b/packages/mcp/package.json
index bb8b5b31..0a5b8093 100644
--- a/packages/mcp/package.json
+++ b/packages/mcp/package.json
@@ -12,8 +12,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "dependencies": {
     "@codeassembly/run-core": "workspace:*",
diff --git a/packages/mcp/src/__tests__/protocol-stdio.test.ts b/packages/mcp/src/__tests__/protocol-stdio.test.ts
index abf3219b..9740085c 100644
--- a/packages/mcp/src/__tests__/protocol-stdio.test.ts
+++ b/packages/mcp/src/__tests__/protocol-stdio.test.ts
@@ -4,7 +4,7 @@ import { dirname, join, resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 
 import { Client } from '@modelcontextprotocol/sdk/client';
-import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio';
+import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js';
 import { describe, expect, it } from 'vitest';
 
 import { isErrorResult, parseAndGetString } from './helpers.ts';
diff --git a/packages/mcp/src/__tests__/protocol.test.ts b/packages/mcp/src/__tests__/protocol.test.ts
index 72119c11..3e703c9b 100644
--- a/packages/mcp/src/__tests__/protocol.test.ts
+++ b/packages/mcp/src/__tests__/protocol.test.ts
@@ -4,7 +4,7 @@ import { join } from 'node:path';
 
 import { v3RunIndexSchema } from '@codeassembly/run-core';
 import { Client } from '@modelcontextprotocol/sdk/client';
-import { InMemoryTransport } from '@modelcontextprotocol/sdk/inMemory';
+import { InMemoryTransport } from '@modelcontextprotocol/sdk/inMemory.js';
 import { afterEach, describe, expect, it } from 'vitest';
 
 import { createServer } from '../server.ts';
diff --git a/packages/mcp/src/__tests__/staleness.test.ts b/packages/mcp/src/__tests__/staleness.test.ts
index f0a97e33..b3defe0f 100644
--- a/packages/mcp/src/__tests__/staleness.test.ts
+++ b/packages/mcp/src/__tests__/staleness.test.ts
@@ -4,7 +4,7 @@ import { join } from 'node:path';
 import { pathToFileURL } from 'node:url';
 
 import { Client } from '@modelcontextprotocol/sdk/client';
-import { InMemoryTransport } from '@modelcontextprotocol/sdk/inMemory';
+import { InMemoryTransport } from '@modelcontextprotocol/sdk/inMemory.js';
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
 
 import { isBuildStale } from '../staleness.ts';
diff --git a/packages/mcp/src/cli.ts b/packages/mcp/src/cli.ts
index d24a41e9..bde01877 100644
--- a/packages/mcp/src/cli.ts
+++ b/packages/mcp/src/cli.ts
@@ -1,6 +1,6 @@
 import process from 'node:process';
 
-import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 
 import { createServer } from './server.ts';
 
diff --git a/packages/mcp/src/server.ts b/packages/mcp/src/server.ts
index 8d1ab5ff..dd2377a9 100644
--- a/packages/mcp/src/server.ts
+++ b/packages/mcp/src/server.ts
@@ -1,4 +1,4 @@
-import { McpServer } from '@modelcontextprotocol/sdk/server/mcp';
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import { z } from 'zod';
 
 import { isBuildStale } from './staleness.ts';
diff --git a/packages/run-core/README.md b/packages/run-core/README.md
index a5a53950..cafa0a8c 100644
--- a/packages/run-core/README.md
+++ b/packages/run-core/README.md
@@ -29,8 +29,6 @@ codeassembly-runs --path <dir>       # override the base projects directory
 
 ### Bin wrapper pattern
 
-The `bin` field in `package.json` points to `bin/codeassembly-runs.js`, a committed wrapper script that dynamically imports the build output at runtime. Do not point `bin` entries directly into `dist/` — pnpm creates bin symlinks during install, before lifecycle scripts like `prepare` run, so the target won't exist in a fresh worktree and `pnpm install` will emit confusing "Failed to create bin" warnings.
-
-If invoked before building, the wrapper finds the entry file absent and tells the user to run `pnpm run build`. It checks for the file directly rather than keying off `ERR_MODULE_NOT_FOUND`, which Node raises for any unresolved module in the graph — including a missing dependency of a build output that is present, where advising a rebuild would be wrong. Any other load failure is reported verbatim.
+The `bin` field in `package.json` points to `bin/codeassembly-runs.js`, a committed wrapper script that dynamically imports the build output at runtime. Do not point `bin` entries directly into `dist/` — pnpm creates bin symlinks during install, and nothing compiles until `pnpm run bootstrap` runs afterward, so the target won't exist in a fresh worktree and `pnpm install` will emit confusing "Failed to create bin" warnings.
 
 Any new `bin` entry in this monorepo should follow the same pattern. See `bin/codeassembly-runs.js` for the template, and the `@williamthorsen/node-monorepo-tools` packages for the original rationale.
diff --git a/packages/run-core/bin/codeassembly-runs.js b/packages/run-core/bin/codeassembly-runs.js
index 6bb21c80..115b2222 100755
--- a/packages/run-core/bin/codeassembly-runs.js
+++ b/packages/run-core/bin/codeassembly-runs.js
@@ -11,7 +11,7 @@ const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
 // module in the graph, so keying the build-first message off the error code would also
 // fire when the build is present and one of its imports is missing.
 if (!existsSync(entryPoint)) {
-  process.stderr.write('codeassembly-runs: build output not found — run `pnpm run build` first\n');
+  process.stderr.write('codeassembly-runs: build output not found — run `pnpm run bootstrap` first\n');
   process.exit(1);
 }
 
diff --git a/packages/run-core/package.json b/packages/run-core/package.json
index 113699fc..8d0731de 100644
--- a/packages/run-core/package.json
+++ b/packages/run-core/package.json
@@ -35,8 +35,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "dependencies": {
     "yaml": "2.9.0",