diff --git a/docs/tools/access-policy.md b/docs/tools/access-policy.md
index 121f2fd6372..fb1504f0f54 100644
--- a/docs/tools/access-policy.md
+++ b/docs/tools/access-policy.md
@@ -130,6 +130,8 @@ For cross-agent MCP tool delegation (an orchestrator invoking a tool on behalf o
 
 **Interpreter bypass of exec bit.** The `x` bit gates `execve()` on the file itself. Running `bash script.sh` executes bash (permitted), which reads the script as text (read permitted if `r` is set). The exec bit on the script is irrelevant for interpreter-based invocations. To prevent execution of a script entirely, place it in the deny list (no read access).
 
+**File-specific `deny[]` entries on Linux (bwrap).** On Linux, `deny[]` entries are enforced at the OS layer using `bwrap --tmpfs` overlays, which only work on directories. When a `deny[]` entry resolves to an existing file (e.g. `deny: ["~/.netrc"]`), the OS-level mount is skipped — bwrap cannot overlay a file with a tmpfs. Tool-layer enforcement still blocks read/write/edit calls for that file. However, exec commands running inside the sandbox can still access the file directly (e.g. `cat ~/.netrc`). A warning is emitted to stderr when this gap is active. To enforce at the OS layer on Linux, deny the parent directory instead (e.g. `deny: ["~/.aws/"]` rather than `deny: ["~/.aws/credentials"]`). On macOS, seatbelt handles file-level denials correctly with `(deny file-read* (literal ...))`.
+
 **No approval flow.** Access policy is fail-closed: a denied operation returns an error immediately. There is no `ask`/`on-miss` mode equivalent to exec approvals. If an agent hits a denied path, it receives a permission error and must handle it. Interactive approval for filesystem access is planned as a follow-up feature.
 
 ## Related
diff --git a/src/infra/access-policy.test.ts b/src/infra/access-policy.test.ts
index 4950a996afb..b4b6b8ffdbf 100644
--- a/src/infra/access-policy.test.ts
+++ b/src/infra/access-policy.test.ts
@@ -865,6 +865,19 @@ describe("applyScriptPolicyOverride", () => {
     }
   });
 
+  it("matches scripts key written with ~ even though resolvedArgv0 is absolute", () => {
+    // Regression: "~/bin/deploy.sh" in scripts{} must match resolvedArgv0 "/home/user/bin/deploy.sh".
+    // A direct object lookup misses tilde keys; ~ must be expanded before comparing.
+    const absPath = path.join(os.homedir(), "bin", "deploy.sh");
+    const base: AccessPolicyConfig = {
+      default: "rwx",
+      scripts: { "~/bin/deploy.sh": { rules: { "/secret/**": "---" } } },
+    };
+    const { overrideRules, hashMismatch } = applyScriptPolicyOverride(base, absPath);
+    expect(hashMismatch).toBeUndefined();
+    expect(overrideRules?.["/secret/**"]).toBe("---");
+  });
+
   it("applies override when sha256 matches — rules in overrideRules, not policy", () => {
     const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "ap-test-"));
     const scriptPath = path.join(tmpDir, "script.sh");
diff --git a/src/infra/access-policy.ts b/src/infra/access-policy.ts
index 821a8b2249b..c86aa2c2cd1 100644
--- a/src/infra/access-policy.ts
+++ b/src/infra/access-policy.ts
@@ -456,7 +456,19 @@ export function applyScriptPolicyOverride(
   policy: AccessPolicyConfig,
   resolvedArgv0: string,
 ): { policy: AccessPolicyConfig; overrideRules?: Record<string, PermStr>; hashMismatch?: true } {
-  const override = policy.scripts?.[resolvedArgv0];
+  // Normalise ~ in scripts keys so "~/bin/deploy.sh" matches the resolved absolute
+  // path "/home/user/bin/deploy.sh" that resolveArgv0 returns. A direct lookup
+  // would always miss tilde-keyed entries, silently skipping sha256 verification.
+  const scripts = policy.scripts;
+  const override = scripts
+    ? (scripts[resolvedArgv0] ??
+      Object.entries(scripts).find(([k]) => {
+        if (!k.startsWith("~")) {
+          return false;
+        }
+        return k.replace(/^~(?=$|[/\\])/, os.homedir()) === resolvedArgv0;
+      })?.[1])
+    : undefined;
   if (!override) {
     return { policy };
   }
diff --git a/src/infra/exec-sandbox-bwrap.test.ts b/src/infra/exec-sandbox-bwrap.test.ts
index 7d1eb0d858c..df771b76f10 100644
--- a/src/infra/exec-sandbox-bwrap.test.ts
+++ b/src/infra/exec-sandbox-bwrap.test.ts
@@ -1,7 +1,11 @@
 import os from "node:os";
-import { describe, expect, it } from "vitest";
+import { describe, expect, it, vi } from "vitest";
 import type { AccessPolicyConfig } from "../config/types.tools.js";
-import { generateBwrapArgs, wrapCommandWithBwrap } from "./exec-sandbox-bwrap.js";
+import {
+  _warnBwrapFileDenyOnce,
+  generateBwrapArgs,
+  wrapCommandWithBwrap,
+} from "./exec-sandbox-bwrap.js";
 
 const HOME = os.homedir();
 
@@ -302,6 +306,19 @@ describe("generateBwrapArgs", () => {
     expect(tmpfsMounts).not.toContain("/etc/hosts");
   });
 
+  it("emits a console.error warning when a file-specific deny[] entry is skipped", () => {
+    // Use /etc/passwd (always a file) rather than /etc/hosts which is already in
+    // _bwrapFileDenyWarnedPaths from the generateBwrapArgs test above.
+    const errSpy = vi.spyOn(console, "error").mockImplementation(() => {});
+    try {
+      _warnBwrapFileDenyOnce("/etc/passwd");
+      expect(errSpy).toHaveBeenCalledWith(expect.stringContaining("/etc/passwd"));
+      expect(errSpy).toHaveBeenCalledWith(expect.stringContaining("parent directory"));
+    } finally {
+      errSpy.mockRestore();
+    }
+  });
+
   it("still emits --tmpfs for deny[] entry that resolves to a directory", () => {
     // Non-existent paths are treated as directories (forward-protection).
     const config: AccessPolicyConfig = { default: "r--", deny: [`${HOME}/.nonexistent-dir/**`] };
diff --git a/src/infra/exec-sandbox-bwrap.ts b/src/infra/exec-sandbox-bwrap.ts
index 7790ae90a15..0c570255597 100644
--- a/src/infra/exec-sandbox-bwrap.ts
+++ b/src/infra/exec-sandbox-bwrap.ts
@@ -26,6 +26,25 @@ const SYSTEM_RO_BIND_PATHS = ["/usr", "/bin", "/lib", "/lib64", "/sbin", "/etc",
 
 let bwrapAvailableCache: boolean | undefined;
 
+// Warn once per process when a file-specific deny[] entry cannot be enforced at
+// the OS layer (bwrap --tmpfs only accepts directories). Tool-layer enforcement
+// still applies for read/write/edit tool calls, but exec commands that access
+// the file directly inside the sandbox are not blocked at the syscall level.
+// See docs/tools/access-policy.md — "File-specific deny[] entries on Linux".
+const _bwrapFileDenyWarnedPaths = new Set<string>();
+export function _warnBwrapFileDenyOnce(filePath: string): void {
+  if (_bwrapFileDenyWarnedPaths.has(filePath)) {
+    return;
+  }
+  _bwrapFileDenyWarnedPaths.add(filePath);
+  console.error(
+    `[access-policy] bwrap: deny[] entry "${filePath}" resolves to a file — ` +
+      `OS-level (bwrap) enforcement is not applied. ` +
+      `Tool-layer enforcement still blocks read/write/edit tool calls. ` +
+      `To protect this file at the OS layer on Linux, deny its parent directory instead.`,
+  );
+}
+
 /**
  * Returns true if bwrap is installed and executable on this system.
  * Result is cached after the first call.
@@ -195,9 +214,12 @@ export function generateBwrapArgs(
     }
     if (isDir) {
       args.push("--tmpfs", p);
+    } else {
+      // File-specific entry: tool-layer checkAccessPolicy still denies read/write/edit
+      // tool calls, but exec commands inside the sandbox can still access the file
+      // directly. Warn operators so they know to deny the parent directory instead.
+      _warnBwrapFileDenyOnce(p);
     }
-    // File-specific entry: tool-layer checkAccessPolicy already denies reads/writes;
-    // bwrap cannot mount tmpfs over a file so skip the OS-layer mount silently.
   }
 
   // Script-specific override mounts — emitted after deny[] so they can reopen