fix(runner): preserve Claude user settings trust in HOME (#17826)

packages/paperclip-runner/README.md

@@ -818,7 +818,10 @@ rules and hooks apply. Native Codex tools can read and modify the execution home
 (read-only for planning); credentials in that home are not isolated from tools.
 Native Codex separately denies Runner-owned protocol state; ACPX Claude retains
 its existing provider trust boundary. Execution is unattended: native Codex uses `never`, and
-ACPX rejects requests for approval. The initial ACPX mode requires the Runner
+ACPX rejects requests for approval. When Claude starts in its home directory,
+its native user settings retain user trust even if the SDK also reports that
+same file as project settings. Other project settings keep the native trust filter.
+The initial ACPX mode requires the Runner
 setting `acpxPermissionMode: "approve-all"` (its default); other Runner modes are
 unqualified here and fail before launch. Local permission rules still apply.
 Preconfigured ACPX read-only/planning tasks also fail before provider launch

packages/paperclip-runner/test/acpx-codex-package-contract.test.mjs

@@ -1,8 +1,11 @@
 import assert from "node:assert/strict";
 import { createHash } from "node:crypto";
-import { readFile } from "node:fs/promises";
+import { execFileSync } from "node:child_process";
+import { mkdtemp, mkdir, readFile, rm, writeFile } from "node:fs/promises";
 import { createRequire } from "node:module";
-import { dirname, resolve } from "node:path";
+import { dirname, join, resolve } from "node:path";
+import { tmpdir } from "node:os";
+import { pathToFileURL } from "node:url";
 import test from "node:test";
 
 const runnerPackage = JSON.parse(
@@ -217,3 +220,39 @@ test("the Claude patch removes ambient project and local configuration", () => {
     );
   }
 });
+
+test("Claude preserves user permission modes when its working directory is home", async (t) => {
+  const packagePath = createRequire(import.meta.url).resolve("@agentclientprotocol/claude-agent-acp/package.json");
+  const settingsModule = pathToFileURL(resolve(dirname(packagePath), "dist/settings.js")).href;
+  const root = await mkdtemp(join(tmpdir(), "claude-settings-origin-"));
+  t.after(() => rm(root, { recursive: true, force: true }));
+  const home = join(root, "home");
+  const project = join(root, "project");
+  await mkdir(join(home, ".claude"), { recursive: true });
+  await mkdir(join(project, ".claude"), { recursive: true });
+  const userFile = join(home, ".claude/settings.json");
+  const env = { ...process.env, HOME: home };
+  delete env.CLAUDE_CONFIG_DIR;
+  delete env.PAPERCLIP_ACPX_ISOLATED_CONTEXT;
+  const inspect = (cwd) => JSON.parse(execFileSync(process.execPath, ["--input-type=module", "-e", `
+    import { SettingsManager } from ${JSON.stringify(settingsModule)};
+    const manager = new SettingsManager(${JSON.stringify(cwd)});
+    try {
+      await manager.initialize();
+      console.log(JSON.stringify(manager.getSettings()));
+    } finally { manager.dispose(); }
+  `], { env, encoding: "utf8", timeout: 10_000 }));
+  for (const defaultMode of ["bypassPermissions", "acceptEdits", "auto", "plan", "default"]) {
+    const content = JSON.stringify({ permissions: { defaultMode, deny: ["Read(./private)"] } });
+    await writeFile(userFile, content);
+    assert.deepEqual(inspect(home).permissions, { defaultMode, deny: ["Read(./private)"] });
+    assert.equal(await readFile(userFile, "utf8"), content, "discovery does not rewrite the profile");
+  }
+  await writeFile(userFile, JSON.stringify({ permissions: { defaultMode: "bypassPermissions" } }));
+  for (const defaultMode of ["bypassPermissions", "acceptEdits", "auto"]) {
+    await writeFile(join(project, ".claude/settings.json"), JSON.stringify({ permissions: { defaultMode } }));
+    assert.equal(inspect(project).permissions?.defaultMode, undefined, "real project escalation stays filtered");
+  }
+  await writeFile(join(home, ".claude/settings.local.json"), JSON.stringify({ permissions: { defaultMode: "plan" } }));
+  assert.equal(inspect(home).permissions.defaultMode, "plan", "local restrictions still win");
+});

patches/@agentclientprotocol__claude-agent-acp@0.73.0.patch

@@ -64,3 +64,19 @@ index 0214a509eb5e7b777a69e4e34637941c275d27b1..403be02df66e25eee29e7d5bef146270
              // Forward MCP elicitation requests onto ACP elicitation. Only attached
              // when the client advertised support, so non-supporting clients keep the
              // SDK's default (auto-decline) behavior. (AskUserQuestion is handled in
+diff --git a/dist/settings.js b/dist/settings.js
+--- a/dist/settings.js
++++ b/dist/settings.js
+@@ -88,6 +88,12 @@
+     async loadAllSettings() {
+         try {
+             const resolved = await resolveSettings({ cwd: this.cwd });
++            const userPath = resolved.sources.find((entry) => entry.source === "user")?.path;
++            for (const entry of resolved.sources) {
++                if (userPath && entry.source === "project" && entry.path === userPath) {
++                    entry.source = "user";
++                }
++            }
+             this.effective = filterEscalatingDefaultMode(resolved);
+         }
+         catch (error) {