diff --git a/.agents/PROJECT.md b/.agents/PROJECT.md
index 78c531e7..87005d51 100644
--- a/.agents/PROJECT.md
+++ b/.agents/PROJECT.md
@@ -31,6 +31,8 @@ MCP server for orchestrated run management. Wraps run-core capabilities as five
 
 **Package:** `@codeassembly/mcp` (private)
 
+**Bin:** `codeassembly-mcp` — the stdio server entry point. `.claude/settings.json` launches the server through `packages/mcp/bin/codeassembly-mcp.js`.
+
 ### Agents (`packages/agents/`)
 
 The agents package is a CLI tool (`codeassembly-agents`) that installs reusable AI skills and subagent definitions into harness-specific directories. It also serves as the canonical home for all skill and subagent content.
@@ -258,12 +260,14 @@ The package README documents the `kb.yaml` configuration schema and merge semant
 
 ### Build system
 
-- Uses esbuild via custom `config/build.ts` for TypeScript packages
-- Intelligent caching based on content hashes
-- Automatic `.ts` to `.js` extension rewriting
-- Alias resolution support (`~src/` -> `src/`)
+- Uses `nmr-compile` (from `@williamthorsen/nmr`) for TypeScript packages, emitting `.js` and `.d.ts` in a single TypeScript pass
+- Intelligent caching based on content hashes, keyed under `node_modules/.cache/nmr-compile/`
+- Automatic `.ts` to `.js` extension rewriting, in compiled output and emitted declarations alike
+- Alias resolution support for `~/`-prefixed imports
 - Factory uses Vite with `@vitejs/plugin-react` for the web app
 
+Deleting `dist/` does not force a rebuild. The build cache lives outside it and is keyed on inputs alone, so a rebuild after a manual delete skips and leaves `dist/` empty. Clear `node_modules/.cache/nmr-compile/` too. Tracked upstream at williamthorsen/node-monorepo-tools#470.
+
 ### TypeScript
 
 - Strict mode across all packages (`strict`, `noUncheckedIndexedAccess`, `exactOptionalPropertyTypes`, `noImplicitReturns`)
diff --git a/.agents/nmr/AGENTS.md b/.agents/nmr/AGENTS.md
index a2243f1e..a32fc50b 100644
--- a/.agents/nmr/AGENTS.md
+++ b/.agents/nmr/AGENTS.md
@@ -1,5 +1,5 @@
 ---
-source: '@williamthorsen/nmr@0.15.0'
+source: '@williamthorsen/nmr@0.18.1'
 ---
 
 # nmr: agent guidance
@@ -38,7 +38,7 @@ Some root scripts (e.g. `lint`, `typecheck`, `test`) expand to `nmr root:X && pn
 
 ## Managed build
 
-The default `compile` script runs `nmr-compile`, a standalone bin that esbuild-compiles a package's `src` to `dist/esm`, rewriting `~/` (package-root) import aliases and `.ts`→`.js` specifiers, and skipping work when inputs are unchanged. There is no repo-local build script to maintain; `nmr build` runs `compile` then `generate-typings`. To find or debug the build, look to `nmr-compile`, not a `config/build.ts` in the consuming repo.
+The default `compile` script runs `nmr-compile`, a standalone bin that uses the TypeScript compiler API to emit a package's `src` to `dist/esm` as `.js` and `.d.ts` in one pass, rewriting relative `.ts`→`.js` specifiers and tsconfig `paths` aliases in both outputs, and skipping work when inputs are unchanged. `typescript` is a peer dependency (`>=5.7.0`). There is no repo-local build script to maintain, and no separate typings step; `nmr build` runs `compile` alone. To find or debug the build, look to `nmr-compile`, not a `config/build.ts` in the consuming repo.
 
 ## Override behaviors
 
diff --git a/.claude/settings.json b/.claude/settings.json
index ee09428b..e015c1bf 100644
--- a/.claude/settings.json
+++ b/.claude/settings.json
@@ -5,7 +5,7 @@
   "mcpServers": {
     "codeassembly": {
       "command": "node",
-      "args": ["packages/mcp/dist/esm/cli.js"]
+      "args": ["packages/mcp/bin/codeassembly-mcp.js"]
     }
   }
 }
diff --git a/config/build.ts b/config/build.ts
deleted file mode 100644
index 8abc491f..00000000
--- a/config/build.ts
+++ /dev/null
@@ -1,106 +0,0 @@
-import { createHash } from 'node:crypto';
-import { existsSync, readFileSync } from 'node:fs';
-import { mkdir, readFile, writeFile } from 'node:fs/promises';
-import path from 'node:path';
-
-import { build, type Format, type Platform, type Plugin } from 'esbuild';
-import { glob } from 'glob';
-
-const CACHE_FILE = 'dist/esm/.cache';
-const format: Format = 'esm';
-const platform: Platform = 'node';
-const target = 'es2022';
-
-const aliases = {
-  '~/src/': 'src/',
-};
-const dependencies = ['package.json'];
-const entryPoints = await glob(['src/**/*.ts'], {
-  ignore: ['**/__tests__/**', '**/test-utils/**'],
-});
-const outputConfig = { format, platform, target: [target] };
-
-if (await hashChanged()) {
-  await build({
-    entryPoints,
-    outdir: 'dist/esm/',
-    bundle: false,
-    sourcemap: false,
-    plugins: [rewriteTsExtensions()],
-    ...outputConfig,
-  });
-}
-
-// region | Helper functions
-async function hashChanged(): Promise<boolean> {
-  const previousHash = existsSync(CACHE_FILE) ? readFileSync(CACHE_FILE, 'utf8') : undefined;
-  const currentHash = await computeHash();
-
-  if (previousHash === currentHash) {
-    console.info('No changes detected. Skipping build.');
-    return false;
-  }
-
-  console.info('Changes detected.');
-  await mkdir(path.dirname(CACHE_FILE), { recursive: true });
-  await writeFile(CACHE_FILE, currentHash);
-  return true;
-}
-
-async function computeHash(): Promise<string> {
-  const hash = createHash('sha256');
-  for (const file of [...entryPoints, ...dependencies]) {
-    const content = await readFile(file);
-    hash.update(content);
-  }
-
-  hash.update(JSON.stringify(outputConfig));
-  return hash.digest('hex');
-}
-
-function rewriteTsExtensions(): Plugin {
-  return {
-    name: 'rewrite-ts-extensions',
-    setup(build) {
-      build.onLoad({ filter: /\.ts$/ }, async (args) => {
-        const fileDir = path.dirname(args.path);
-        let code = await readFile(args.path, 'utf8');
-
-        code = resolveAliasImports(code, fileDir, aliases);
-        code = rewriteTsImportExtensions(code);
-
-        return { contents: code, loader: 'ts' };
-      });
-    },
-  };
-}
-
-/**
- * Rewrites alias import paths to relative filesystem paths from the importing file.
- *
- * @param code - The TypeScript source code.
- * @param fileDir - The absolute path to the importing file’s directory.
- * @param aliasMap - A map of alias prefixes (e.g. '@/') to base paths (e.g. 'src/').
- */
-function resolveAliasImports(code: string, fileDir: string, aliasMap: Record<string, string>): string {
-  for (const [alias, targetDir] of Object.entries(aliasMap)) {
-    const escaped = alias.replaceAll(/[.*+?^${}()|[\]\\]/g, String.raw`\$&`); // escape regex
-    const regex = new RegExp(String.raw`(?<=from\s+['"])${escaped}([^'"]+)(?=['"])`, 'g');
-
-    code = code.replace(regex, (_, subpath: string) => {
-      const absolute = path.resolve(targetDir, subpath);
-      const relative = path.relative(fileDir, absolute);
-      return relative.startsWith('.') ? relative : `./${relative}`;
-    });
-  }
-
-  return code;
-}
-
-/**
- * Rewrites relative imports ending in `.ts` to `.js` to match compiled output.
- */
-function rewriteTsImportExtensions(code: string): string {
-  return code.replaceAll(/(?<=from\s+['"])(\.{1,2}\/[^'"]+)\.ts(?=['"])/g, '$1.js');
-}
-// endregion | Helper functions
diff --git a/package.json b/package.json
index bffa4db3..37de9ab0 100644
--- a/package.json
+++ b/package.json
@@ -34,11 +34,10 @@
     "@vitest/coverage-v8": "4.1.10",
     "@vitest/eslint-plugin": "1.6.23",
     "@williamthorsen/eslint-config-typescript": "5.17.6",
-    "@williamthorsen/nmr": "0.16.0",
+    "@williamthorsen/nmr": "0.18.1",
     "@williamthorsen/release-kit": "8.0.0",
     "@williamthorsen/strict-lint": "6.3.2",
     "dotenv": "17.4.2",
-    "esbuild": "0.28.1",
     "eslint": "9.39.5",
     "eslint-plugin-import": "2.32.0",
     "eslint-plugin-jest-dom": "5.5.0",
diff --git a/packages/agents/bin/codeassembly-agents.js b/packages/agents/bin/codeassembly-agents.js
index 615f8f63..02293471 100755
--- a/packages/agents/bin/codeassembly-agents.js
+++ b/packages/agents/bin/codeassembly-agents.js
@@ -1,15 +1,24 @@
 #!/usr/bin/env node
 
+import { existsSync } from 'node:fs';
+
 // Thin wrapper so pnpm can symlink the bin at install time, before `dist/`
 // exists. The real entry point loads at runtime from the build output.
 // See packages/run-core/README.md ("Bin wrapper pattern") for details.
+const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
+
+// Gate on the entry file itself: Node raises ERR_MODULE_NOT_FOUND for any unresolved
+// 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.exit(1);
+}
+
 try {
-  await import('../dist/esm/cli.js');
+  await import(entryPoint.href);
 } catch (error) {
-  if (error.code === 'ERR_MODULE_NOT_FOUND') {
-    process.stderr.write('codeassembly-agents: build output not found — run `pnpm run build` first\n');
-  } else {
-    process.stderr.write(`codeassembly-agents: failed to load: ${error.message}\n`);
-  }
+  const message = error instanceof Error ? error.message : String(error);
+  process.stderr.write(`codeassembly-agents: failed to load: ${message}\n`);
   process.exit(1);
 }
diff --git a/packages/agents/package.json b/packages/agents/package.json
index 86ce6fbf..4d359f78 100644
--- a/packages/agents/package.json
+++ b/packages/agents/package.json
@@ -25,7 +25,8 @@
   },
   "devDependencies": {
     "@hyperjump/json-schema": "1.17.7",
-    "@williamthorsen/toolbelt.strings": "3.1.4"
+    "@williamthorsen/toolbelt.strings": "3.1.4",
+    "esbuild": "0.28.1"
   },
   "engines": {
     "node": ">=24"
diff --git a/packages/kb/bin/kb.js b/packages/kb/bin/kb.js
index 6b561afd..2824bd3d 100755
--- a/packages/kb/bin/kb.js
+++ b/packages/kb/bin/kb.js
@@ -1,16 +1,24 @@
 #!/usr/bin/env node
 
+import { existsSync } from 'node:fs';
+
 // Thin wrapper so pnpm can symlink the bin at install time, before `dist/` exists.
 // The real entry point loads at runtime from the build output.
 // See packages/run-core/README.md ("Bin wrapper pattern") for details.
+const entryPoint = new URL('../dist/esm/cli/index.js', import.meta.url);
+
+// Gate on the entry file itself: Node raises ERR_MODULE_NOT_FOUND for any unresolved
+// 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.exit(1);
+}
+
 try {
-  await import('../dist/esm/cli/index.js');
+  await import(entryPoint.href);
 } catch (error) {
-  if (error.code === 'ERR_MODULE_NOT_FOUND') {
-    process.stderr.write('kb: build output not found — run `pnpm run build` first\n');
-  } else {
-    const message = error instanceof Error ? error.message : String(error);
-    process.stderr.write(`kb: failed to load: ${message}\n`);
-  }
+  const message = error instanceof Error ? error.message : String(error);
+  process.stderr.write(`kb: failed to load: ${message}\n`);
   process.exit(1);
 }
diff --git a/packages/kb/package.json b/packages/kb/package.json
index dc1719d0..1cc736ce 100644
--- a/packages/kb/package.json
+++ b/packages/kb/package.json
@@ -76,8 +76,8 @@
     "!dist/esm/test-utils"
   ],
   "scripts": {
-    "build": "nmr compile && nmr generate-typings",
-    "prepare": "nmr compile && nmr generate-typings"
+    "build": "nmr compile",
+    "prepare": "nmr compile"
   },
   "dependencies": {
     "picomatch": "4.0.5",
diff --git a/packages/kb/tsconfig.generate-typings.json b/packages/kb/tsconfig.generate-typings.json
deleted file mode 100644
index cc9c8982..00000000
--- a/packages/kb/tsconfig.generate-typings.json
+++ /dev/null
@@ -1,13 +0,0 @@
-// TSConfig for declaration emit. esbuild owns the .js; tsc owns only the .d.ts.
-{
-  "$schema": "https://json.schemastore.org/tsconfig",
-  "extends": "./tsconfig.json",
-  "compilerOptions": {
-    "emitDeclarationOnly": true,
-    "noEmit": false,
-    "outDir": "./dist/esm",
-  },
-  // Tests and their support code are not part of the published type surface.
-  "exclude": ["**/__tests__/**", "**/*.test.ts", "src/test-utils/"],
-  "include": ["src/"],
-}
diff --git a/packages/mcp/bin/codeassembly-mcp.js b/packages/mcp/bin/codeassembly-mcp.js
new file mode 100755
index 00000000..fd7e0a62
--- /dev/null
+++ b/packages/mcp/bin/codeassembly-mcp.js
@@ -0,0 +1,24 @@
+#!/usr/bin/env node
+
+import { existsSync } from 'node:fs';
+
+// Committed launch path for the stdio server, so `.claude/settings.json` targets a file that
+// exists before `dist/` is built. The real entry point loads at runtime from the build output.
+// See packages/run-core/README.md ("Bin wrapper pattern") for details.
+const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
+
+// Gate on the entry file itself: Node raises ERR_MODULE_NOT_FOUND for any unresolved
+// 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.exit(1);
+}
+
+try {
+  await import(entryPoint.href);
+} catch (error) {
+  const message = error instanceof Error ? error.message : String(error);
+  process.stderr.write(`codeassembly-mcp: failed to load: ${message}\n`);
+  process.exit(1);
+}
diff --git a/packages/mcp/package.json b/packages/mcp/package.json
index f1004431..f9cf953c 100644
--- a/packages/mcp/package.json
+++ b/packages/mcp/package.json
@@ -4,6 +4,13 @@
   "private": true,
   "description": "MCP server for orchestrated run management",
   "type": "module",
+  "bin": {
+    "codeassembly-mcp": "bin/codeassembly-mcp.js"
+  },
+  "files": [
+    "bin",
+    "dist"
+  ],
   "scripts": {
     "build": "nmr compile",
     "prepare": "nmr compile"
diff --git a/packages/run-core/README.md b/packages/run-core/README.md
index af7e15b2..a5a53950 100644
--- a/packages/run-core/README.md
+++ b/packages/run-core/README.md
@@ -31,6 +31,6 @@ codeassembly-runs --path <dir>       # override the base projects directory
 
 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 detects `ERR_MODULE_NOT_FOUND` and tells the user to run `pnpm run build`.
+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.
 
 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 b5e6fad5..6bb21c80 100755
--- a/packages/run-core/bin/codeassembly-runs.js
+++ b/packages/run-core/bin/codeassembly-runs.js
@@ -1,15 +1,24 @@
 #!/usr/bin/env node
 
+import { existsSync } from 'node:fs';
+
 // Thin wrapper so pnpm can symlink the bin at install time, before `dist/`
 // exists. The real entry point loads at runtime from the build output.
 // See packages/run-core/README.md ("Bin wrapper pattern") for details.
+const entryPoint = new URL('../dist/esm/cli.js', import.meta.url);
+
+// Gate on the entry file itself: Node raises ERR_MODULE_NOT_FOUND for any unresolved
+// 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.exit(1);
+}
+
 try {
-  await import('../dist/esm/cli.js');
+  await import(entryPoint.href);
 } catch (error) {
-  if (error.code === 'ERR_MODULE_NOT_FOUND') {
-    process.stderr.write('codeassembly-runs: build output not found — run `pnpm run build` first\n');
-  } else {
-    process.stderr.write(`codeassembly-runs: failed to load: ${error.message}\n`);
-  }
+  const message = error instanceof Error ? error.message : String(error);
+  process.stderr.write(`codeassembly-runs: failed to load: ${message}\n`);
   process.exit(1);
 }
diff --git a/packages/run-core/package.json b/packages/run-core/package.json
index f0597766..c1f524c6 100644
--- a/packages/run-core/package.json
+++ b/packages/run-core/package.json
@@ -35,8 +35,8 @@
     "dist"
   ],
   "scripts": {
-    "build": "nmr compile && nmr generate-typings",
-    "prepare": "nmr compile && nmr generate-typings"
+    "build": "nmr compile",
+    "prepare": "nmr compile"
   },
   "dependencies": {
     "yaml": "2.9.0",
diff --git a/packages/run-core/tsconfig.generate-typings.json b/packages/run-core/tsconfig.generate-typings.json
deleted file mode 100644
index eab75a69..00000000
--- a/packages/run-core/tsconfig.generate-typings.json
+++ /dev/null
@@ -1,13 +0,0 @@
-// TSConfig for declaration emit. esbuild owns the .js; tsc owns only the .d.ts.
-{
-  "$schema": "https://json.schemastore.org/tsconfig",
-  "extends": "./tsconfig.json",
-  "compilerOptions": {
-    "emitDeclarationOnly": true,
-    "noEmit": false,
-    "outDir": "./dist/esm",
-  },
-  // Tests are not part of the published type surface.
-  "exclude": ["**/__tests__/**", "**/*.test.ts"],
-  "include": ["src/"],
-}
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 9b3a186b..f3297455 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -33,8 +33,8 @@ importers:
         specifier: 5.17.6
         version: 5.17.6(@types/estree@1.0.8)(@typescript-eslint/utils@8.64.0(eslint@9.39.5(jiti@2.7.0))(typescript@5.9.3))(eslint@9.39.5(jiti@2.7.0))(typescript@5.9.3)
       '@williamthorsen/nmr':
-        specifier: 0.16.0
-        version: 0.16.0
+        specifier: 0.18.1
+        version: 0.18.1(typescript@5.9.3)
       '@williamthorsen/release-kit':
         specifier: 8.0.0
         version: 8.0.0
@@ -44,9 +44,6 @@ importers:
       dotenv:
         specifier: 17.4.2
         version: 17.4.2
-      esbuild:
-        specifier: 0.28.1
-        version: 0.28.1
       eslint:
         specifier: 9.39.5
         version: 9.39.5(jiti@2.7.0)
@@ -114,6 +111,9 @@ importers:
       '@williamthorsen/toolbelt.strings':
         specifier: 3.1.4
         version: 3.1.4
+      esbuild:
+        specifier: 0.28.1
+        version: 0.28.1
 
   packages/factory:
     dependencies:
@@ -1139,15 +1139,14 @@ packages:
       eslint: '>=9'
       typescript: '>=5'
 
-  '@williamthorsen/nmr-core@0.5.0':
-    resolution: {integrity: sha512-7Jdo+IdZ2lsY7hNV+/zbU2TdL8TJNZFGKBEo43N6jfBaPNfoWHBqRouW+O9CZf1OdzkTbfxmPcs/PBbnIWYD3g==}
-
   '@williamthorsen/nmr-core@0.7.0':
     resolution: {integrity: sha512-0Go/8helfB+nXldaAt6z9lDpV0m7gu9tZ8rrmu2KhEVGeH3VrnLB83wNwm41lZffmooC5tkj3cD3Z04xzt6yJg==}
 
-  '@williamthorsen/nmr@0.16.0':
-    resolution: {integrity: sha512-lPZ58Jt2JSF2eAFUoiOEIBhTwkgdR9eNZKVk0K22tnB5T/e6kaeiaxUQ46bDK/T9urjYMniAfYYPs8iJFjk6MQ==}
+  '@williamthorsen/nmr@0.18.1':
+    resolution: {integrity: sha512-wEXadR7+jQiPZnjuCSiiAAj3GD4IRQ3hKAH2b96HEWDxRytg6DeFU7uLZlS1wSmg9DSLmo4Hdg6Y/d8BOOqzdA==}
     hasBin: true
+    peerDependencies:
+      typescript: '>=5.7.0'
 
   '@williamthorsen/release-kit@8.0.0':
     resolution: {integrity: sha512-MYAC5QmoDtzIiN01H1rjZrQZREQYbh13S+CTY3f+YDt2QnkMDbHSTdGsI84CEcEz4VuQyiHkU12vdtPkW5rYyQ==}
@@ -4282,16 +4281,14 @@ snapshots:
       - '@types/estree'
       - supports-color
 
-  '@williamthorsen/nmr-core@0.5.0': {}
-
   '@williamthorsen/nmr-core@0.7.0': {}
 
-  '@williamthorsen/nmr@0.16.0':
+  '@williamthorsen/nmr@0.18.1(typescript@5.9.3)':
     dependencies:
-      '@williamthorsen/nmr-core': 0.5.0
-      esbuild: 0.28.1
+      '@williamthorsen/nmr-core': 0.7.0
       glob: 13.0.6
       jiti: 2.7.0
+      typescript: 5.9.3
       yaml: 2.9.0
       zod: 4.4.3