fix(coding-agent): respect package.json pi.extensions manifest in settings extensions paths

collectAutoExtensionEntries now checks if the directory itself has a
package.json with pi.extensions (or index.ts) before scanning children.
This fixes duplicate extension loading when a manifest-aware directory
is specified directly in settings.json extensions array.

Fixes #1274

packages/coding-agent/CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- Fixed extensions setting not respecting `package.json` `pi.extensions` manifest when directory is specified directly ([#1302](https://github.com/badlogic/pi-mono/pull/1302) by [@hjanuschka](https://github.com/hjanuschka))
+
 ## [0.52.3] - 2026-02-05
 
 ### Fixed

packages/coding-agent/src/core/package-manager.ts

@@ -402,6 +402,13 @@ function collectAutoExtensionEntries(dir: string): string[] {
 	const entries: string[] = [];
 	if (!existsSync(dir)) return entries;
 
+	// First check if this directory itself has explicit extension entries (package.json or index)
+	const rootEntries = resolveExtensionEntries(dir);
+	if (rootEntries) {
+		return rootEntries;
+	}
+
+	// Otherwise, discover extensions from directory contents
 	const ig = ignore();
 	addIgnoreRules(ig, dir, dir);
 

packages/coding-agent/test/package-manager.test.ts

@@ -111,6 +111,40 @@ Content`,
 			const result = await packageManager.resolve();
 			expect(result.prompts.some((r) => r.path === promptPath && !r.enabled)).toBe(true);
 		});
+
+		it("should resolve directory with package.json pi.extensions in extensions setting", async () => {
+			// Create a package with pi.extensions in package.json
+			const pkgDir = join(tempDir, "my-extensions-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "my-extensions-pkg",
+					pi: {
+						extensions: ["./extensions/clip.ts", "./extensions/cost.ts"],
+					},
+				}),
+			);
+			writeFileSync(join(pkgDir, "extensions", "clip.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "cost.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "helper.ts"), "export const x = 1;"); // Not in manifest, shouldn't be loaded
+
+			// Add the directory to extensions setting (not packages setting)
+			settingsManager.setExtensionPaths([pkgDir]);
+
+			const result = await packageManager.resolve();
+
+			// Should find the extensions declared in package.json pi.extensions
+			expect(result.extensions.some((r) => r.path === join(pkgDir, "extensions", "clip.ts") && r.enabled)).toBe(
+				true,
+			);
+			expect(result.extensions.some((r) => r.path === join(pkgDir, "extensions", "cost.ts") && r.enabled)).toBe(
+				true,
+			);
+
+			// Should NOT find helper.ts (not declared in manifest)
+			expect(result.extensions.some((r) => r.path.endsWith("helper.ts"))).toBe(false);
+		});
 	});
 
 	describe("ignore files", () => {