fix: preserve external settings.json edits on reload (#1046)

Co-authored-by: Mario Zechner <badlogicgames@gmail.com>

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

@@ -0,0 +1,99 @@
+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", () => {
+		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");
+
+		// 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", () => {
+		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");
+
+		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"]);
+	});
+});