diff --git a/patches/libuv/win-poll-abort-with-disconnect.patch b/patches/libuv/win-poll-abort-with-disconnect.patch
index 92b49ffaeaa2..d22fef59a8ec 100644
--- a/patches/libuv/win-poll-abort-with-disconnect.patch
+++ b/patches/libuv/win-poll-abort-with-disconnect.patch
@@ -1,5 +1,3 @@
-diff --git a/src/win/poll.c b/src/win/poll.c
-index ecc6cf3..361b0fc 100644
 --- a/src/win/poll.c
 +++ b/src/win/poll.c
 @@ -115,7 +115,12 @@ static void uv__fast_poll_submit_poll_req(uv_loop_t* loop, uv_poll_t* handle) {
diff --git a/scripts/build/fetch-cli.ts b/scripts/build/fetch-cli.ts
index 63d06d5fb8c4..cc5119cb2ddb 100644
--- a/scripts/build/fetch-cli.ts
+++ b/scripts/build/fetch-cli.ts
@@ -24,7 +24,7 @@ import { spawnSync } from "node:child_process";
 import { createHash } from "node:crypto";
 import { existsSync, readFileSync } from "node:fs";
 import { mkdir, readFile, rm, writeFile } from "node:fs/promises";
-import { basename, join } from "node:path";
+import { basename, dirname, join } from "node:path";
 import { downloadWithRetry, extractTarGz, fetchPrebuilt } from "./download.ts";
 import { BuildError, assert } from "./error.ts";
 import { writeIfChanged } from "./fs.ts";
@@ -242,13 +242,32 @@ function normalizeLf(s: string): string {
  * so a CRLF-mangled checkout still applies cleanly. --no-index: dest/ is
  * not a git repo. --ignore-whitespace / --ignore-space-change: patches are
  * authored against upstream which may have different trailing whitespace.
+ *
+ * GIT_CEILING_DIRECTORIES stops git from discovering the enclosing bun
+ * repo. Without it, `--no-index` still runs setup_git_directory(), finds
+ * the bun repo, and for a patch with a `diff --git a/... b/...` header
+ * treats its paths as TOPLEVEL-relative ("When running from a subdirectory
+ * in a repository, patched paths outside the directory are ignored" —
+ * git-apply(1)): `src/foo.c` is outside the `vendor/<dep>/` prefix, so git
+ * reports `Skipped patch '...'` (only under -v) and exits 0 having changed
+ * nothing — the .ref stamp then certifies an unpatched tree. Plain unified
+ * diffs (`--- a/X` / `+++ b/X` with no header) are resolved cwd-relative
+ * instead, which is why most of patches/ went unaffected.
+ *
+ * The skip check below is belt-and-suspenders against any remaining
+ * exit-0-but-skipped case. It needs -v (git only prints the skip message
+ * above normal verbosity) and LC_ALL=C (the message goes through gettext).
  */
-function applyPatch(dest: string, patchPath: string, patchBody: string): void {
-  const result = spawnSync("git", ["apply", "--ignore-whitespace", "--ignore-space-change", "--no-index", "-"], {
+export function applyPatch(dest: string, patchPath: string, patchBody: string): void {
+  // Inherited GIT_DIR/GIT_WORK_TREE (git hooks, some CI wrappers) bypass
+  // ceiling-based discovery entirely and reintroduce the skip.
+  const { GIT_DIR: _d, GIT_WORK_TREE: _w, ...env } = process.env;
+  const result = spawnSync("git", ["apply", "-v", "--ignore-whitespace", "--ignore-space-change", "--no-index", "-"], {
     cwd: dest,
     input: normalizeLf(patchBody),
     stdio: ["pipe", "ignore", "pipe"],
     encoding: "utf8",
+    env: { ...env, GIT_CEILING_DIRECTORIES: dirname(dest), LC_ALL: "C" },
   });
 
   if (result.error) {
@@ -264,6 +283,16 @@ function applyPatch(dest: string, patchPath: string, patchBody: string): void {
       hint: "The patch may be out of date with the pinned commit",
     });
   }
+
+  // Defense-in-depth: a file git decides is outside the worktree is
+  // skipped with exit 0. Nothing under patches/ is ever meant to be
+  // skipped — if it fires, GIT_CEILING_DIRECTORIES above didn't take.
+  if (result.stderr.includes("Skipped patch")) {
+    throw new BuildError(`git apply silently skipped a file:\n${result.stderr.trim()}`, {
+      file: patchPath,
+      hint: "The patch path resolved outside the dep source dir; see applyPatch() in fetch-cli.ts",
+    });
+  }
 }
 
 // Only run if this file is the entry point (not imported as a module).
diff --git a/test/internal/dep-patch-apply.test.ts b/test/internal/dep-patch-apply.test.ts
new file mode 100644
index 000000000000..5a7ab1736875
--- /dev/null
+++ b/test/internal/dep-patch-apply.test.ts
@@ -0,0 +1,98 @@
+/**
+ * Regression tests for scripts/build/fetch-cli.ts::applyPatch: `git apply`
+ * from a repo subdirectory treats `diff --git` patch paths as toplevel-
+ * relative and silently skips them with exit 0 (git-apply(1)). See the
+ * doc comment on applyPatch for the full mechanism.
+ */
+import { describe, expect, test } from "bun:test";
+import { tempDir } from "harness";
+import { spawnSync } from "node:child_process";
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+import { applyPatch } from "../../scripts/build/fetch-cli.ts";
+
+const ORIGINAL = "line one\nline two\nline three\n";
+const PATCHED = "line one\nline two (patched)\nline three\n";
+
+/** A patch with a `diff --git` header, the form that tripped the bug. */
+const GIT_HEADER_PATCH = `diff --git a/src/file.c b/src/file.c
+index 1111111..2222222 100644
+--- a/src/file.c
++++ b/src/file.c
+@@ -1,3 +1,3 @@
+ line one
+-line two
++line two (patched)
+ line three
+`;
+
+/** The same change as a plain unified diff (what most of patches/ uses). */
+const PLAIN_PATCH = `--- a/src/file.c
++++ b/src/file.c
+@@ -1,3 +1,3 @@
+ line one
+-line two
++line two (patched)
+ line three
+`;
+
+/** git repo → vendor/<dep>/src/file.c; returns the `dest` fetch-cli passes. */
+function makeDepTree(): { dir: ReturnType<typeof tempDir>; dest: string; target: string } {
+  const dir = tempDir("apply-patch", {
+    "vendor/mydep/src/file.c": ORIGINAL,
+  });
+  // Repo above dest is the precondition for the toplevel-relative rewrite.
+  const init = spawnSync("git", ["init", "-q"], { cwd: String(dir), encoding: "utf8" });
+  if (init.status !== 0) throw new Error(`git init failed: ${init.stderr}`);
+  const dest = join(String(dir), "vendor", "mydep");
+  return { dir, dest, target: join(dest, "src", "file.c") };
+}
+
+describe("applyPatch (scripts/build/fetch-cli.ts)", () => {
+  test("applies a diff --git patch from a repo subdirectory", () => {
+    const { dir, dest, target } = makeDepTree();
+    using _ = dir;
+
+    // Pre-fix: "Skipped patch 'src/file.c'." (only under -v), exit 0, file untouched.
+    applyPatch(dest, "test.patch", GIT_HEADER_PATCH);
+
+    expect(readFileSync(target, "utf8")).toBe(PATCHED);
+  });
+
+  test("applies a plain unified diff from a repo subdirectory", () => {
+    const { dir, dest, target } = makeDepTree();
+    using _ = dir;
+
+    applyPatch(dest, "test.patch", PLAIN_PATCH);
+
+    expect(readFileSync(target, "utf8")).toBe(PATCHED);
+  });
+
+  test("a patch that does not apply is reported as an error", () => {
+    const { dir, dest } = makeDepTree();
+    using _ = dir;
+
+    const bad = GIT_HEADER_PATCH.replace("-line two\n", "-does not exist\n");
+    expect(() => applyPatch(dest, "test.patch", bad)).toThrow(/Patch failed/);
+  });
+
+  test("ignores inherited GIT_DIR / GIT_WORK_TREE", () => {
+    // These (set by git hooks) bypass GIT_CEILING_DIRECTORIES entirely.
+    const { dir, dest, target } = makeDepTree();
+    using _ = dir;
+
+    const saved = { GIT_DIR: process.env.GIT_DIR, GIT_WORK_TREE: process.env.GIT_WORK_TREE };
+    process.env.GIT_DIR = join(String(dir), ".git");
+    process.env.GIT_WORK_TREE = String(dir);
+    try {
+      applyPatch(dest, "test.patch", GIT_HEADER_PATCH);
+      expect(readFileSync(target, "utf8")).toBe(PATCHED);
+    } finally {
+      for (const [k, v] of Object.entries(saved)) {
+        if (v === undefined) delete process.env[k];
+        else process.env[k] = v;
+      }
+    }
+  });
+});