move pi-mono into companion-cloud as apps/companion-os

- Copy all pi-mono source into apps/companion-os/
- Update Dockerfile to COPY pre-built binary instead of downloading from GitHub Releases
- Update deploy-staging.yml to build pi from source (bun compile) before Docker build
- Add apps/companion-os/** to path triggers
- No more cross-repo dispatch needed

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

packages/coding-agent/test/settings-manager-bug.test.ts

@@ -0,0 +1,165 @@
+import { existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from "fs";
+import { join } from "path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { SettingsManager } from "../src/core/settings-manager.js";
+
+/**
+ * Tests for the fix to a bug where external file changes to arrays were overwritten.
+ *
+ * The bug scenario was:
+ * 1. Pi starts with settings.json containing packages: ["npm:some-pkg"]
+ * 2. User externally edits file to packages: []
+ * 3. User changes an unrelated setting (e.g., theme) via UI
+ * 4. save() would overwrite packages back to ["npm:some-pkg"] from stale in-memory state
+ *
+ * The fix tracks which fields were explicitly modified during the session, and only
+ * those fields override file values during save().
+ */
+describe("SettingsManager - External Edit Preservation", () => {
+  const testDir = join(process.cwd(), "test-settings-bug-tmp");
+  const agentDir = join(testDir, "agent");
+  const projectDir = join(testDir, "project");
+
+  beforeEach(() => {
+    if (existsSync(testDir)) {
+      rmSync(testDir, { recursive: true });
+    }
+    mkdirSync(agentDir, { recursive: true });
+    mkdirSync(join(projectDir, ".pi"), { recursive: true });
+  });
+
+  afterEach(() => {
+    if (existsSync(testDir)) {
+      rmSync(testDir, { recursive: true });
+    }
+  });
+
+  it("should preserve file changes to packages array when changing unrelated setting", async () => {
+    const settingsPath = join(agentDir, "settings.json");
+
+    // Initial state: packages has one item
+    writeFileSync(
+      settingsPath,
+      JSON.stringify({
+        theme: "dark",
+        packages: ["npm:pi-mcp-adapter"],
+      }),
+    );
+
+    // Pi starts up, loads settings into memory
+    const manager = SettingsManager.create(projectDir, agentDir);
+
+    // At this point, globalSettings.packages = ["npm:pi-mcp-adapter"]
+    expect(manager.getPackages()).toEqual(["npm:pi-mcp-adapter"]);
+
+    // User externally edits settings.json to remove the package
+    const currentSettings = JSON.parse(readFileSync(settingsPath, "utf-8"));
+    currentSettings.packages = []; // User wants to remove this!
+    writeFileSync(settingsPath, JSON.stringify(currentSettings, null, 2));
+
+    // Verify file was changed
+    expect(JSON.parse(readFileSync(settingsPath, "utf-8")).packages).toEqual(
+      [],
+    );
+
+    // User changes an UNRELATED setting via UI (this triggers save)
+    manager.setTheme("light");
+    await manager.flush();
+
+    // With the fix, packages should be preserved as [] (not reverted to startup value)
+    const savedSettings = JSON.parse(readFileSync(settingsPath, "utf-8"));
+
+    expect(savedSettings.packages).toEqual([]);
+    expect(savedSettings.theme).toBe("light");
+  });
+
+  it("should preserve file changes to extensions array when changing unrelated setting", async () => {
+    const settingsPath = join(agentDir, "settings.json");
+
+    writeFileSync(
+      settingsPath,
+      JSON.stringify({
+        theme: "dark",
+        extensions: ["/old/extension.ts"],
+      }),
+    );
+
+    const manager = SettingsManager.create(projectDir, agentDir);
+
+    // User externally updates extensions
+    const currentSettings = JSON.parse(readFileSync(settingsPath, "utf-8"));
+    currentSettings.extensions = ["/new/extension.ts"];
+    writeFileSync(settingsPath, JSON.stringify(currentSettings, null, 2));
+
+    // Change unrelated setting
+    manager.setDefaultThinkingLevel("high");
+    await manager.flush();
+
+    const savedSettings = JSON.parse(readFileSync(settingsPath, "utf-8"));
+
+    // With the fix, extensions should be preserved (not reverted to startup value)
+    expect(savedSettings.extensions).toEqual(["/new/extension.ts"]);
+  });
+
+  it("should preserve external project settings changes when updating unrelated project field", async () => {
+    const projectSettingsPath = join(projectDir, ".pi", "settings.json");
+    writeFileSync(
+      projectSettingsPath,
+      JSON.stringify({
+        extensions: ["./old-extension.ts"],
+        prompts: ["./old-prompt.md"],
+      }),
+    );
+
+    const manager = SettingsManager.create(projectDir, agentDir);
+
+    const currentProjectSettings = JSON.parse(
+      readFileSync(projectSettingsPath, "utf-8"),
+    );
+    currentProjectSettings.prompts = ["./new-prompt.md"];
+    writeFileSync(
+      projectSettingsPath,
+      JSON.stringify(currentProjectSettings, null, 2),
+    );
+
+    manager.setProjectExtensionPaths(["./updated-extension.ts"]);
+    await manager.flush();
+
+    const savedProjectSettings = JSON.parse(
+      readFileSync(projectSettingsPath, "utf-8"),
+    );
+    expect(savedProjectSettings.prompts).toEqual(["./new-prompt.md"]);
+    expect(savedProjectSettings.extensions).toEqual(["./updated-extension.ts"]);
+  });
+
+  it("should let in-memory project changes override external changes for the same project field", async () => {
+    const projectSettingsPath = join(projectDir, ".pi", "settings.json");
+    writeFileSync(
+      projectSettingsPath,
+      JSON.stringify({
+        extensions: ["./initial-extension.ts"],
+      }),
+    );
+
+    const manager = SettingsManager.create(projectDir, agentDir);
+
+    const currentProjectSettings = JSON.parse(
+      readFileSync(projectSettingsPath, "utf-8"),
+    );
+    currentProjectSettings.extensions = ["./external-extension.ts"];
+    writeFileSync(
+      projectSettingsPath,
+      JSON.stringify(currentProjectSettings, null, 2),
+    );
+
+    manager.setProjectExtensionPaths(["./in-memory-extension.ts"]);
+    await manager.flush();
+
+    const savedProjectSettings = JSON.parse(
+      readFileSync(projectSettingsPath, "utf-8"),
+    );
+    expect(savedProjectSettings.extensions).toEqual([
+      "./in-memory-extension.ts",
+    ]);
+  });
+});