diff --git a/gitnexus/src/core/embeddings/embedder.ts b/gitnexus/src/core/embeddings/embedder.ts
index d873f3a0a3..3ec5f08e16 100644
--- a/gitnexus/src/core/embeddings/embedder.ts
+++ b/gitnexus/src/core/embeddings/embedder.ts
@@ -28,6 +28,7 @@ import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
 import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry } from './hf-env.js';
 import { getLocalEmbeddingRuntimeBlocker } from './runtime-support.js';
+import { ensureOnnxRuntimeCommonResolvable } from './onnxruntime-common-resolver.js';
 import { logger } from '../logger.js';
 
 /**
@@ -179,6 +180,9 @@ export const initEmbedder = async (
     try {
       // Lazy-load transformers.js only after the runtime guard has passed, so
       // unsupported platforms never reach the native ONNX import (#1515).
+      // Under pnpm-strict / `pnpm dlx`, transformers' phantom `onnxruntime-common`
+      // import is unresolvable; register the fallback resolver first (#307).
+      ensureOnnxRuntimeCommonResolvable();
       const { pipeline, env } = await import('@huggingface/transformers');
 
       // Configure transformers.js environment
diff --git a/gitnexus/src/core/embeddings/onnxruntime-common-resolver.ts b/gitnexus/src/core/embeddings/onnxruntime-common-resolver.ts
new file mode 100644
index 0000000000..fbb4f40823
--- /dev/null
+++ b/gitnexus/src/core/embeddings/onnxruntime-common-resolver.ts
@@ -0,0 +1,133 @@
+/**
+ * Make `@huggingface/transformers`' phantom `onnxruntime-common` import
+ * resolvable under strict package-manager layouts (#307, #2069).
+ *
+ * ## Why
+ * transformers' shipped `dist/transformers.node.mjs` does a bare
+ * `import 'onnxruntime-common'`, but transformers' `package.json` never declares
+ * onnxruntime-common (it lists onnxruntime-node / onnxruntime-web / sharp). With
+ * npm's flat `node_modules` — or pnpm with hoisting — the package is hoisted to
+ * a directory on transformers' resolution path and the import resolves by
+ * accident. Under pnpm's isolated store (and therefore `pnpm dlx` / `pnpx`), a
+ * package only sees its *declared* deps, so the import dies with
+ * `ERR_MODULE_NOT_FOUND` before `analyze --embeddings` can run.
+ *
+ * Declaring onnxruntime-common in gitnexus' own dependencies (#2074) does NOT
+ * fix this under pnpm: Node resolves the bare specifier from *transformers'*
+ * module scope, not ours, and overrides/resolutions can only re-version an
+ * existing edge, never add the missing one.
+ *
+ * ## What this does
+ * Install a synchronous, in-thread ESM resolution hook (`module.registerHooks`,
+ * Node >= 22.15) that redirects `onnxruntime-common` to a copy gitnexus can
+ * resolve — but only when the default resolver fails. The redirect target is
+ * preferentially the `onnxruntime-common` that `onnxruntime-node` (the native
+ * binding transformers actually loads) itself depends on, so the redirected copy
+ * is version-matched to that binding even under `pnpm dlx` — where gitnexus'
+ * npm-style `overrides` block does NOT apply, because it is honoured only from a
+ * root manifest and gitnexus is a transitive dependency there. It falls back to
+ * gitnexus' own direct `onnxruntime-common` dependency when that chain can't be
+ * walked. onnxruntime-common is a stable, pure-JS package whose `Tensor` surface
+ * is unchanged across 1.24–1.26, so either target is API-compatible. On working
+ * layouts the default resolver succeeds first and the hook never fires, so
+ * behaviour is unchanged.
+ *
+ * `registerHooks` (synchronous, in-thread) is preferred over the older
+ * `module.register` (async, off-thread, now deprecated — DEP0205, removed in
+ * Node 26): the redirect is a one-line conditional that needs no worker thread,
+ * no separate hook module, and no `data` marshalling.
+ *
+ * ## Safety
+ * Best-effort and idempotent. The hook is installed lazily, only on the
+ * local-embedding code path (after parsing), so it is never registered during
+ * analysis, in the parse workers, or in HTTP embedding mode. Once installed it
+ * is process-global: its resolve closure runs for every subsequent module
+ * resolution, but it passes all of them through untouched and only substitutes a
+ * result for the exact `onnxruntime-common` specifier when that specifier is
+ * genuinely absent — so it cannot mask an unrelated resolution error, and the
+ * per-resolution cost is a single string comparison.
+ *
+ * `module.registerHooks` is marked `@experimental` and requires Node >= 22.15
+ * (the gitnexus engines floor is >= 22.0.0). On older runtimes it is absent and
+ * this is a graceful no-op: embeddings then resolve onnxruntime-common exactly
+ * as before — fine on hoisted layouts. Any failure during installation is
+ * swallowed.
+ */
+import { registerHooks, createRequire } from 'node:module';
+import { pathToFileURL } from 'node:url';
+import { logger } from '../logger.js';
+
+let attempted = false;
+
+/**
+ * Compute the file: URL the hook redirects `onnxruntime-common` to.
+ *
+ * Prefer the copy `onnxruntime-node` (the native binding transformers loads)
+ * depends on, so the redirected module is version-matched to the binding even
+ * under `pnpm dlx`, where transformers keeps its own pinned onnxruntime-node.
+ * The walk resolves transformers' MAIN entry — NOT `@huggingface/transformers/
+ * package.json`, which transformers' `exports` map blocks
+ * (`ERR_PACKAGE_PATH_NOT_EXPORTED`) — then onnxruntime-node, then its
+ * onnxruntime-common. Falls back to gitnexus' own direct dependency (always
+ * resolvable from our scope) when any step fails.
+ */
+const resolveOnnxRuntimeCommonUrl = (): string => {
+  const require = createRequire(import.meta.url);
+  try {
+    const transformersMain = require.resolve('@huggingface/transformers');
+    const ortNodePkg = createRequire(transformersMain).resolve('onnxruntime-node/package.json');
+    const common = createRequire(ortNodePkg).resolve('onnxruntime-common');
+    return pathToFileURL(common).href;
+  } catch {
+    return pathToFileURL(require.resolve('onnxruntime-common')).href;
+  }
+};
+
+/**
+ * Idempotently install the onnxruntime-common resolution fallback. Call once
+ * immediately before the dynamic `import('@huggingface/transformers')` on the
+ * local-embedding path.
+ */
+export const ensureOnnxRuntimeCommonResolvable = (): void => {
+  if (attempted) return;
+  // Mark attempted up-front: a failed attempt must not retry on every
+  // initEmbedder() call, and the hook is process-global — once is enough.
+  attempted = true;
+
+  try {
+    // Node < 22.15 (the gitnexus engines floor is >= 22.0.0): no synchronous
+    // hooks API. Degrade gracefully — the import still works on hoisted layouts.
+    if (typeof registerHooks !== 'function') return;
+
+    const redirectUrl = resolveOnnxRuntimeCommonUrl();
+
+    registerHooks({
+      resolve(specifier, context, nextResolve) {
+        if (specifier !== 'onnxruntime-common') return nextResolve(specifier, context);
+        // Honour a real, package-manager-provided copy when one is on the path
+        // (npm / hoisted pnpm); only substitute ours when the specifier is
+        // genuinely absent.
+        try {
+          return nextResolve(specifier, context);
+        } catch (err) {
+          // The phantom import surfaces as ERR_MODULE_NOT_FOUND (or, for a
+          // present-but-exports-broken copy, ERR_PACKAGE_PATH_NOT_EXPORTED).
+          // Rethrow anything else so a genuinely broken install is not masked.
+          const code = (err as { code?: string } | null | undefined)?.code;
+          if (code === 'ERR_MODULE_NOT_FOUND' || code === 'ERR_PACKAGE_PATH_NOT_EXPORTED') {
+            return { url: redirectUrl, shortCircuit: true };
+          }
+          throw err;
+        }
+      },
+    });
+    logger.debug({ redirectUrl }, 'Installed onnxruntime-common resolution fallback (#307)');
+  } catch (err) {
+    // Never block embeddings on the fallback. On layouts where the package
+    // manager already resolves onnxruntime-common this is unnecessary anyway.
+    logger.debug(
+      { err: err instanceof Error ? err.message : String(err) },
+      'onnxruntime-common resolution fallback not installed',
+    );
+  }
+};
diff --git a/gitnexus/src/mcp/core/embedder.ts b/gitnexus/src/mcp/core/embedder.ts
index 451d12c1f8..4dd73f317a 100644
--- a/gitnexus/src/mcp/core/embedder.ts
+++ b/gitnexus/src/mcp/core/embedder.ts
@@ -22,6 +22,7 @@ import {
   withHfDownloadRetry,
 } from '../../core/embeddings/hf-env.js';
 import { getLocalEmbeddingRuntimeBlocker } from '../../core/embeddings/runtime-support.js';
+import { ensureOnnxRuntimeCommonResolvable } from '../../core/embeddings/onnxruntime-common-resolver.js';
 import { silenceStdout, restoreStdout, realStderrWrite } from '../../core/lbug/pool-adapter.js';
 
 import { logger } from '../../core/logger.js';
@@ -65,6 +66,9 @@ export const initEmbedder = async (): Promise<FeatureExtractionPipeline> => {
     try {
       // Lazy-load transformers.js only after the runtime guard has passed, so
       // unsupported platforms never reach the native ONNX import (#1515).
+      // Under pnpm-strict / `pnpm dlx`, transformers' phantom `onnxruntime-common`
+      // import is unresolvable; register the fallback resolver first (#307).
+      ensureOnnxRuntimeCommonResolvable();
       const { pipeline, env } = await import('@huggingface/transformers');
 
       env.allowLocalModels = false;
diff --git a/gitnexus/test/unit/onnxruntime-common-resolver.test.ts b/gitnexus/test/unit/onnxruntime-common-resolver.test.ts
new file mode 100644
index 0000000000..801cb001ee
--- /dev/null
+++ b/gitnexus/test/unit/onnxruntime-common-resolver.test.ts
@@ -0,0 +1,132 @@
+import { describe, it, expect, vi, afterEach } from 'vitest';
+
+/**
+ * Tests for the #307 pnpm-strict / `pnpm dlx` fix: a synchronous in-thread ESM
+ * resolution hook (`module.registerHooks`) that redirects @huggingface/
+ * transformers' phantom `onnxruntime-common` import to gitnexus' own copy.
+ *
+ * Each test mocks `node:module` with a chosen `registerHooks` (a spy, or
+ * `undefined` to simulate Node < 22.15) so we can assert one-shot installation,
+ * graceful degradation, and the redirect/passthrough/rethrow logic of the
+ * resolve closure — without mutating the real process loader.
+ */
+
+const RESOLVER = '../../src/core/embeddings/onnxruntime-common-resolver.js';
+
+/**
+ * (Re)load the resolver with a chosen `registerHooks` mocked into node:module.
+ * `vi.resetModules()` + the fresh `import()` re-initialises the module-level
+ * one-shot guard, so each test gets a pristine resolver with no shared state.
+ */
+async function loadResolver(registerHooks: unknown) {
+  vi.resetModules();
+  vi.doMock('node:module', async (importOriginal) => {
+    const orig = await importOriginal<typeof import('node:module')>();
+    return { ...orig, registerHooks };
+  });
+  return import(RESOLVER);
+}
+
+const ctx = { conditions: [], importAttributes: {} } as never;
+const moduleNotFound = (): Error => {
+  const e = new Error("Cannot find package 'onnxruntime-common'") as Error & { code: string };
+  e.code = 'ERR_MODULE_NOT_FOUND';
+  return e;
+};
+
+afterEach(() => {
+  vi.doUnmock('node:module');
+});
+
+describe('ensureOnnxRuntimeCommonResolvable — installation', () => {
+  it('installs the resolve hook exactly once (idempotent)', async () => {
+    const spy = vi.fn();
+    const mod = await loadResolver(spy);
+
+    mod.ensureOnnxRuntimeCommonResolvable();
+    mod.ensureOnnxRuntimeCommonResolvable(); // second call is a no-op
+
+    expect(spy).toHaveBeenCalledTimes(1);
+    expect(typeof spy.mock.calls[0][0].resolve).toBe('function');
+  });
+
+  it('no-ops gracefully when registerHooks is unavailable (Node < 22.15)', async () => {
+    const mod = await loadResolver(undefined);
+    // Must not throw even though there is no synchronous-hooks API to call.
+    expect(() => mod.ensureOnnxRuntimeCommonResolvable()).not.toThrow();
+  });
+
+  it('is best-effort: swallows a registerHooks() failure instead of throwing into the embedder', async () => {
+    const mod = await loadResolver(
+      vi.fn(() => {
+        throw new Error('hook-install-failed');
+      }),
+    );
+    // The call site (initEmbedder) does not guard the return; a throw here would
+    // break `analyze --embeddings`. The outer try/catch must absorb it.
+    expect(() => mod.ensureOnnxRuntimeCommonResolvable()).not.toThrow();
+  });
+});
+
+describe('ensureOnnxRuntimeCommonResolvable — resolve hook behaviour', () => {
+  /** Install the fallback and return the resolve closure handed to registerHooks. */
+  async function captureResolve() {
+    const spy = vi.fn();
+    const mod = await loadResolver(spy);
+    mod.ensureOnnxRuntimeCommonResolvable();
+    return spy.mock.calls[0][0].resolve as (
+      s: string,
+      c: never,
+      n: (s: string, c: never) => unknown,
+    ) => unknown;
+  }
+
+  it('passes a successful default resolution through unchanged (no-op on hoisted layouts)', async () => {
+    const resolve = await captureResolve();
+    const real = { url: 'file:///real/onnxruntime-common/index.js', shortCircuit: true };
+    const next = vi.fn(() => real);
+
+    const res = resolve('onnxruntime-common', ctx, next);
+
+    expect(next).toHaveBeenCalledTimes(1);
+    expect(res).toBe(real); // the real resolution, NOT a redirect
+  });
+
+  it('redirects onnxruntime-common to the gitnexus copy when default resolution fails', async () => {
+    const resolve = await captureResolve();
+    const next = vi.fn(() => {
+      throw moduleNotFound();
+    });
+
+    const res = resolve('onnxruntime-common', ctx, next) as { url: string; shortCircuit: boolean };
+
+    expect(res.shortCircuit).toBe(true);
+    // The real resolved onnxruntime-common in node_modules (require.resolve runs
+    // for real here) — not just any path containing the substring.
+    expect(res.url).toMatch(/^file:\/\/.*\/node_modules\/onnxruntime-common\/.*\.js$/);
+  });
+
+  it('never masks an unrelated resolution failure (other specifiers rethrow)', async () => {
+    const resolve = await captureResolve();
+    const err = moduleNotFound();
+    const next = vi.fn(() => {
+      throw err;
+    });
+
+    expect(() => resolve('some-other-package', ctx, next)).toThrow(err);
+  });
+
+  it('rethrows when onnxruntime-common fails for a non-absence reason', async () => {
+    const resolve = await captureResolve();
+    // A present-but-otherwise-broken resolution (not a missing package) must
+    // surface, not be silently papered over with gitnexus' copy.
+    const err = Object.assign(new Error('bad specifier'), {
+      code: 'ERR_INVALID_MODULE_SPECIFIER',
+    });
+    const next = vi.fn(() => {
+      throw err;
+    });
+
+    expect(() => resolve('onnxruntime-common', ctx, next)).toThrow(err);
+  });
+});