fix: prefer cursor native hooks during install

scripts/lib/install-targets/cursor-project.js

@@ -29,6 +29,7 @@ module.exports = createInstallTargetAdapter({
     const modules = Array.isArray(input.modules)
       ? input.modules
       : (input.module ? [input.module] : []);
+    const seenDestinationPaths = new Set();
     const {
       repoRoot,
       projectRoot,
@@ -40,20 +41,66 @@ module.exports = createInstallTargetAdapter({
       homeDir,
     };
     const targetRoot = adapter.resolveRoot(planningInput);
-
+    const entries = modules.flatMap((module, moduleIndex) => {
-    return modules.flatMap(module => {
       const paths = Array.isArray(module.paths) ? module.paths : [];
       return paths
         .filter(p => !isForeignPlatformPath(p, adapter.target))
-        .flatMap(sourceRelativePath => {
+        .map((sourceRelativePath, pathIndex) => ({
+          module,
+          sourceRelativePath,
+          moduleIndex,
+          pathIndex,
+        }));
+    }).sort((left, right) => {
+      const getPriority = value => {
+        if (value === 'rules') {
+          return 0;
+        }
+
+        if (value === '.cursor') {
+          return 1;
+        }
+
+        return 2;
+      };
+
+      const leftPriority = getPriority(left.sourceRelativePath);
+      const rightPriority = getPriority(right.sourceRelativePath);
+      if (leftPriority !== rightPriority) {
+        return leftPriority - rightPriority;
+      }
+
+      if (left.moduleIndex !== right.moduleIndex) {
+        return left.moduleIndex - right.moduleIndex;
+      }
+
+      return left.pathIndex - right.pathIndex;
+    });
+
+    function takeUniqueOperations(operations) {
+      return operations.filter(operation => {
+        if (!operation || !operation.destinationPath) {
+          return false;
+        }
+
+        if (seenDestinationPaths.has(operation.destinationPath)) {
+          return false;
+        }
+
+        seenDestinationPaths.add(operation.destinationPath);
+        return true;
+      });
+    }
+
+    return entries.flatMap(({ module, sourceRelativePath }) => {
       if (sourceRelativePath === 'rules') {
-            return createFlatRuleOperations({
+        return takeUniqueOperations(createFlatRuleOperations({
           moduleId: module.id,
           repoRoot,
           sourceRelativePath,
           destinationDir: path.join(targetRoot, 'rules'),
           destinationNameTransform: toCursorRuleFileName,
-            });
+        }));
       }
 
       if (sourceRelativePath === '.cursor') {
@@ -80,11 +127,12 @@ module.exports = createInstallTargetAdapter({
           destinationNameTransform: toCursorRuleFileName,
         });
 
-            return [...childOperations, ...ruleOperations];
+        return takeUniqueOperations([...childOperations, ...ruleOperations]);
       }
 
-          return [adapter.createScaffoldOperation(module.id, sourceRelativePath, planningInput)];
+      return takeUniqueOperations([
-        });
+        adapter.createScaffoldOperation(module.id, sourceRelativePath, planningInput),
+      ]);
     });
   },
 });

tests/lib/install-manifests.test.js

@@ -124,11 +124,11 @@ function runTests() {
     );
     assert.ok(
       plan.operations.some(operation => (
-        operation.sourceRelativePath === '.cursor/rules/common-agents.md'
+        operation.sourceRelativePath === 'rules/common/agents.md'
         && operation.destinationPath === path.join(projectRoot, '.cursor', 'rules', 'common-agents.mdc')
         && operation.strategy === 'flatten-copy'
       )),
-      'Should flatten Cursor platform rules into .mdc files'
+      'Should produce Cursor .mdc rules while preferring rules-core over duplicate platform copies'
     );
   })) passed++; else failed++;
 

tests/lib/install-targets.test.js

@@ -209,6 +209,70 @@ function runTests() {
     );
   })) passed++; else failed++;
 
+  if (test('deduplicates cursor rule destinations when rules-core and platform-configs overlap', () => {
+    const repoRoot = path.join(__dirname, '..', '..');
+    const projectRoot = '/workspace/app';
+
+    const plan = planInstallTargetScaffold({
+      target: 'cursor',
+      repoRoot,
+      projectRoot,
+      modules: [
+        {
+          id: 'rules-core',
+          paths: ['rules'],
+        },
+        {
+          id: 'platform-configs',
+          paths: ['.cursor'],
+        },
+      ],
+    });
+
+    const commonAgentsDestinations = plan.operations.filter(operation => (
+      operation.destinationPath === path.join(projectRoot, '.cursor', 'rules', 'common-agents.mdc')
+    ));
+
+    assert.strictEqual(commonAgentsDestinations.length, 1, 'Should keep only one common-agents.mdc operation');
+    assert.strictEqual(
+      normalizedRelativePath(commonAgentsDestinations[0].sourceRelativePath),
+      'rules/common/agents.md',
+      'Should prefer rules-core when cursor platform rules would collide'
+    );
+  })) passed++; else failed++;
+
+  if (test('prefers native cursor hooks when hooks-runtime and platform-configs overlap', () => {
+    const repoRoot = path.join(__dirname, '..', '..');
+    const projectRoot = '/workspace/app';
+
+    const plan = planInstallTargetScaffold({
+      target: 'cursor',
+      repoRoot,
+      projectRoot,
+      modules: [
+        {
+          id: 'hooks-runtime',
+          paths: ['hooks', 'scripts/hooks', 'scripts/lib'],
+        },
+        {
+          id: 'platform-configs',
+          paths: ['.cursor'],
+        },
+      ],
+    });
+
+    const hooksDestinations = plan.operations.filter(operation => (
+      operation.destinationPath === path.join(projectRoot, '.cursor', 'hooks')
+    ));
+
+    assert.strictEqual(hooksDestinations.length, 1, 'Should keep only one .cursor/hooks scaffold operation');
+    assert.strictEqual(
+      normalizedRelativePath(hooksDestinations[0].sourceRelativePath),
+      '.cursor/hooks',
+      'Should prefer native Cursor hooks over generic hooks-runtime hooks'
+    );
+  })) passed++; else failed++;
+
   if (test('plans antigravity remaps for workflows, skills, and flat rules', () => {
     const repoRoot = path.join(__dirname, '..', '..');
     const projectRoot = '/workspace/app';