#1095 Move compilation out of the install lifecycle into a bootstrap step

.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)

.config/wt.toml

@@ -3,4 +3,4 @@
 [post-create]
 direnv = "direnv allow"
 deps = "pnpm install"
-build = "nmr build"
+bootstrap = "pnpm run bootstrap"

.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

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)
 ```

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"
   },

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);
 }
 

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);
 }
 

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",

packages/lifecycle/package.json

@@ -16,8 +16,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "devDependencies": {
     "esbuild": "0.28.1"

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);
 }
 

packages/mcp/package.json

@@ -12,8 +12,7 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile",
-    "prepare": "nmr compile"
+    "build": "nmr compile"
   },
   "dependencies": {
     "@codeassembly/run-core": "workspace:*",

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';

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';

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';

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';
 

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';

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.

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);
 }
 

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",