diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index a121a117..b2c4320a 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- Empty array in package filter now disables all resources instead of falling back to manifest defaults ([#1044](https://github.com/badlogic/pi-mono/issues/1044))
+
 ## [0.50.1] - 2026-01-26
 
 ### Fixed
diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index a91c587b..ebb9be04 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -1155,17 +1155,17 @@ export class DefaultPackageManager implements PackageManager {
 		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
 		metadata: PathMetadata,
 	): void {
-		const { allFiles, enabledByManifest } = this.collectManifestFiles(packageRoot, resourceType);
+		const { allFiles } = this.collectManifestFiles(packageRoot, resourceType);
 
 		if (userPatterns.length === 0) {
-			// No user patterns, just use manifest filtering
+			// Empty array explicitly disables all resources of this type
 			for (const f of allFiles) {
-				this.addResource(target, f, metadata, enabledByManifest.has(f));
+				this.addResource(target, f, metadata, false);
 			}
 			return;
 		}
 
-		// Apply user patterns on top of manifest-enabled files
+		// Apply user patterns
 		const enabledByUser = applyPatterns(allFiles, userPatterns, packageRoot);
 
 		for (const f of allFiles) {