diff --git a/plugins/plugin-agent-orchestrator/__tests__/unit/workspace-diff.test.ts b/plugins/plugin-agent-orchestrator/__tests__/unit/workspace-diff.test.ts
index 473ed45416d68..33f4e6b4aa538 100644
--- a/plugins/plugin-agent-orchestrator/__tests__/unit/workspace-diff.test.ts
+++ b/plugins/plugin-agent-orchestrator/__tests__/unit/workspace-diff.test.ts
@@ -1,5 +1,5 @@
 import { execFileSync } from "node:child_process";
-import { mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
@@ -8,6 +8,7 @@ import {
   captureBaselineDirty,
   captureBaselineSha,
   captureChangeSet,
+  parseLsFiles,
   summarizeChangeSet,
   verifyChangedFilesOnDisk,
 } from "../../src/services/workspace-diff.ts";
@@ -304,3 +305,81 @@ describe("workspace-diff — unborn HEAD + untracked (#11578)", () => {
     expect(cs).toBeUndefined();
   });
 });
+
+// The unborn-HEAD untracked scoop (37813124bf, #11605) could flood the
+// MAX_CHANGED_FILES cap and evict the agent's real files:
+// 1. a fresh scaffold that runs `npm install` BEFORE writing .gitignore has
+//    thousands of untracked node_modules paths (`--exclude-standard` has no
+//    .gitignore to honor yet), all of which entered the scoop;
+// 2. agent-written tool paths were spread LAST into the changed-files union,
+//    and Set dedupe keeps first-occurrence order, so the flood evicted them.
+describe("workspace-diff — unborn-HEAD scoop flood (#11605)", () => {
+  let dir: string;
+
+  beforeEach(() => {
+    dir = mkdtempSync(join(tmpdir(), "wsdiff-flood-"));
+    git(dir, ["init", "-q"]);
+    git(dir, ["config", "user.email", "t@t.t"]);
+    git(dir, ["config", "user.name", "t"]);
+    // NO initial commit — HEAD is unborn. NO .gitignore — install ran first.
+  });
+
+  afterEach(() => {
+    rmSync(dir, { recursive: true, force: true });
+  });
+
+  it("filters vendor install output that predates any .gitignore", async () => {
+    // Shell-scaffolded app (no tool paths at all) + `npm install` output.
+    writeFileSync(join(dir, "index.html"), "<h1>app</h1>\n");
+    writeFileSync(join(dir, "package.json"), "{}\n");
+    writeFileSync(join(dir, "server.js"), "require('http');\n");
+    for (let i = 0; i < 120; i++) {
+      const pkg = join(
+        dir,
+        "node_modules",
+        `pkg-${String(i).padStart(3, "0")}`,
+      );
+      mkdirSync(pkg, { recursive: true });
+      writeFileSync(join(pkg, "index.js"), "module.exports={};\n");
+    }
+    const cs = await captureChangeSet(dir);
+    expect(cs).toBeDefined();
+    // ls-files sorts node_modules/* between index.html and package.json —
+    // without the vendor filter the cap kept index.html + 59 node_modules
+    // paths and evicted package.json and server.js entirely.
+    expect(cs?.changedFiles).toContain("index.html");
+    expect(cs?.changedFiles).toContain("package.json");
+    expect(cs?.changedFiles).toContain("server.js");
+    expect(cs?.changedFiles.some((f) => f.startsWith("node_modules/"))).toBe(
+      false,
+    );
+  });
+
+  it("agent-written files survive the cap ahead of a large scaffold", async () => {
+    // More legit untracked files than MAX_CHANGED_FILES, all sorting before
+    // the agent's tool-written file.
+    for (let i = 0; i < 70; i++) {
+      writeFileSync(
+        join(dir, `page-${String(i).padStart(2, "0")}.html`),
+        "<p></p>\n",
+      );
+    }
+    writeFileSync(join(dir, "zzz-server.js"), "require('http');\n");
+    const cs = await captureChangeSet(dir, undefined, ["zzz-server.js"]);
+    expect(cs).toBeDefined();
+    // agentWritten-first: the explicit tool write leads the list and cannot
+    // be evicted by the cap (previously it sat at position 71 and was cut).
+    expect(cs?.changedFiles[0]).toBe("zzz-server.js");
+    expect(cs?.changedFiles.length).toBeLessThanOrEqual(60);
+    expect(cs?.truncated).toBe(true);
+  });
+
+  it("parseLsFiles drops the truncated garbage tail of an over-maxBuffer listing", () => {
+    // A complete `git ls-files` listing always ends with a newline; output cut
+    // at maxBuffer (ENOBUFS) ends mid-path instead.
+    expect(parseLsFiles("a.txt\nb.txt\nnode_mod")).toEqual(["a.txt", "b.txt"]);
+    expect(parseLsFiles("a.txt\nb.txt\n")).toEqual(["a.txt", "b.txt"]);
+    expect(parseLsFiles("partial-only-no-newline")).toEqual([]);
+    expect(parseLsFiles(undefined)).toEqual([]);
+  });
+});
diff --git a/plugins/plugin-agent-orchestrator/src/services/workspace-diff.ts b/plugins/plugin-agent-orchestrator/src/services/workspace-diff.ts
index 19cf2142de99c..589118873c6af 100644
--- a/plugins/plugin-agent-orchestrator/src/services/workspace-diff.ts
+++ b/plugins/plugin-agent-orchestrator/src/services/workspace-diff.ts
@@ -157,14 +157,55 @@ function parseNameStatus(out: string | undefined): string[] {
   return files;
 }
 
-/** Parse `git ls-files --others` output (one path per line) into a path list. */
-function parseLsFiles(out: string | undefined): string[] {
-  return (out ?? "")
+/**
+ * Parse `git ls-files --others` output (one path per line) into a path list.
+ * A complete listing always ends with a newline; when the output was cut at
+ * maxBuffer (ENOBUFS on a huge untracked tree) the tail is a truncated
+ * garbage path — drop the partial final line rather than surface junk.
+ */
+export function parseLsFiles(out: string | undefined): string[] {
+  if (!out) return [];
+  const complete = out.endsWith("\n")
+    ? out
+    : out.slice(0, out.lastIndexOf("\n") + 1);
+  return complete
     .split("\n")
     .map((line) => line.trim())
     .filter((line) => line.length > 0);
 }
 
+// Dependency/build directories a fresh scaffold populates BEFORE any
+// .gitignore exists (`npm install` typically runs first). On an unborn HEAD
+// `--exclude-standard` has no .gitignore to honor, so thousands of vendor
+// paths would flood MAX_CHANGED_FILES and evict the agent's real files.
+// Fallback for the unborn-HEAD untracked scoop ONLY — the born-HEAD path
+// never scoops untracked files, and explicit tool-written paths are always
+// kept regardless (agentWritten is unioned separately).
+const UNBORN_SCOOP_VENDOR_DIRS = new Set([
+  "node_modules",
+  ".git",
+  ".yarn",
+  ".pnpm-store",
+  ".venv",
+  "venv",
+  "__pycache__",
+  ".cache",
+  ".turbo",
+  ".next",
+  ".nuxt",
+  "dist",
+  "build",
+  "coverage",
+  "vendor",
+  "target",
+]);
+
+function isVendorScoopPath(path: string): boolean {
+  return path
+    .split("/")
+    .some((segment) => UNBORN_SCOOP_VENDOR_DIRS.has(segment));
+}
+
 /**
  * Resolve the base ref for the completion diff. Prefers the captured baseline
  * sha; otherwise HEAD — but when HEAD is unborn (a fresh repo with zero commits)
@@ -279,11 +320,15 @@ export async function captureChangeSet(
   const untracked = unbornHead
     ? parseLsFiles(
         await git(workdir, ["ls-files", "--others", "--exclude-standard"]),
-      ).filter((file) => !dirtyAtSpawn.has(file))
+      ).filter((file) => !dirtyAtSpawn.has(file) && !isVendorScoopPath(file))
     : [];
 
+  // Agent-written paths FIRST: explicit edit/write tool calls are the
+  // highest-signal entries and must survive the MAX_CHANGED_FILES cap when a
+  // large scaffold floods `untracked`. Set dedupe keeps first-occurrence
+  // order, so spreading them last let the flood evict them entirely.
   const changedFiles = [
-    ...new Set([...tracked, ...untracked, ...agentWritten]),
+    ...new Set([...agentWritten, ...tracked, ...untracked]),
   ].slice(0, MAX_CHANGED_FILES);
   if (changedFiles.length === 0) return undefined;