diff --git a/scripts/lib/install-targets/claude-home.js b/scripts/lib/install-targets/claude-home.js
index 5cc426ac9..2de35ec58 100644
--- a/scripts/lib/install-targets/claude-home.js
+++ b/scripts/lib/install-targets/claude-home.js
@@ -1,6 +1,7 @@
 const path = require('path');
 
 const {
+  HOME_INSTALL_EXCLUDED_SOURCE_PATHS,
   createInstallTargetAdapter,
   createRemappedOperation,
   isForeignPlatformPath,
@@ -52,6 +53,7 @@ module.exports = createInstallTargetAdapter({
   kind: 'home',
   rootSegments: ['.claude'],
   installStatePathSegments: ['ecc', 'install-state.json'],
+  excludedSourcePaths: HOME_INSTALL_EXCLUDED_SOURCE_PATHS,
   nativeRootRelativePath: '.claude-plugin',
   planOperations(input, adapter) {
     const modules = Array.isArray(input.modules)
@@ -66,7 +68,7 @@ module.exports = createInstallTargetAdapter({
     return modules.flatMap(module => {
       const paths = Array.isArray(module.paths) ? module.paths : [];
       return paths
-        .filter(p => !isForeignPlatformPath(p, adapter.target))
+        .filter(p => !isForeignPlatformPath(p, adapter.target) && !adapter.excludesSourcePath(p))
         .flatMap(sourceRelativePath => {
           if (
             module.id === 'hooks-runtime'
diff --git a/scripts/lib/install-targets/codex-home.js b/scripts/lib/install-targets/codex-home.js
index ae29b41a1..aff32c4c5 100644
--- a/scripts/lib/install-targets/codex-home.js
+++ b/scripts/lib/install-targets/codex-home.js
@@ -1,4 +1,4 @@
-const { createInstallTargetAdapter } = require('./helpers');
+const { HOME_INSTALL_EXCLUDED_SOURCE_PATHS, createInstallTargetAdapter } = require('./helpers');
 
 module.exports = createInstallTargetAdapter({
   id: 'codex-home',
@@ -7,4 +7,5 @@ module.exports = createInstallTargetAdapter({
   rootSegments: ['.codex'],
   installStatePathSegments: ['ecc-install-state.json'],
   nativeRootRelativePath: '.codex',
+  excludedSourcePaths: HOME_INSTALL_EXCLUDED_SOURCE_PATHS,
 });
diff --git a/scripts/lib/install-targets/helpers.js b/scripts/lib/install-targets/helpers.js
index f69d75e86..5df5ae1c4 100644
--- a/scripts/lib/install-targets/helpers.js
+++ b/scripts/lib/install-targets/helpers.js
@@ -24,6 +24,14 @@ const PLATFORM_SOURCE_PATH_OWNERS = Object.freeze({
   '.adal': 'adal',
 });
 
+// Source paths that home installs must never copy into a harness home
+// directory. `.agents` is ECC's repo-local skills/plugins staging area:
+// project targets such as kimi and antigravity consume it, but neither
+// Claude Code nor Codex reads a `.agents` directory under ~/.claude or
+// ~/.codex, so copying it there produces unread files that doctor flags as
+// drift and repair keeps restoring.
+const HOME_INSTALL_EXCLUDED_SOURCE_PATHS = Object.freeze(['.agents']);
+
 function normalizeRelativePath(relativePath) {
   return String(relativePath || '')
     .replace(/\\/g, '/')
@@ -43,6 +51,14 @@ function isForeignPlatformPath(sourceRelativePath, adapterTarget) {
   return false;
 }
 
+function isExcludedSourcePath(sourceRelativePath, excludedSourcePaths = []) {
+  const normalizedPath = normalizeRelativePath(sourceRelativePath);
+  return excludedSourcePaths.some(excluded => {
+    const prefix = normalizeRelativePath(excluded);
+    return prefix !== '' && (normalizedPath === prefix || normalizedPath.startsWith(`${prefix}/`));
+  });
+}
+
 function resolveBaseRoot(scope, input = {}) {
   if (scope === 'home') {
     return input.homeDir || os.homedir();
@@ -351,6 +367,9 @@ function createInstallTargetAdapter(config) {
         strategy: adapter.determineStrategy(normalizedSourcePath),
       });
     },
+    excludesSourcePath(sourceRelativePath) {
+      return isExcludedSourcePath(sourceRelativePath, config.excludedSourcePaths);
+    },
     planOperations(input = {}) {
       if (typeof config.planOperations === 'function') {
         return config.planOperations(input, adapter);
@@ -360,7 +379,7 @@ function createInstallTargetAdapter(config) {
         return input.modules.flatMap(module => {
           const paths = Array.isArray(module.paths) ? module.paths : [];
           return paths
-            .filter(p => !isForeignPlatformPath(p, config.target))
+            .filter(p => !isForeignPlatformPath(p, config.target) && !adapter.excludesSourcePath(p))
             .map(sourceRelativePath => adapter.createScaffoldOperation(
               module.id,
               sourceRelativePath,
@@ -372,7 +391,7 @@ function createInstallTargetAdapter(config) {
       const module = input.module || {};
       const paths = Array.isArray(module.paths) ? module.paths : [];
       return paths
-        .filter(p => !isForeignPlatformPath(p, config.target))
+        .filter(p => !isForeignPlatformPath(p, config.target) && !adapter.excludesSourcePath(p))
         .map(sourceRelativePath => adapter.createScaffoldOperation(
           module.id,
           sourceRelativePath,
@@ -399,6 +418,8 @@ function createInstallTargetAdapter(config) {
 }
 
 module.exports = {
+  HOME_INSTALL_EXCLUDED_SOURCE_PATHS,
+  isExcludedSourcePath,
   buildValidationIssue,
   createFlatFileOperations,
   createFlatRuleOperations,
diff --git a/tests/scripts/install-apply.test.js b/tests/scripts/install-apply.test.js
index 270339cb9..c1e935dcc 100644
--- a/tests/scripts/install-apply.test.js
+++ b/tests/scripts/install-apply.test.js
@@ -593,6 +593,54 @@ function runTests() {
     }
   })) passed++; else failed++;
 
+  if (test('home installs do not copy the repo .agents staging directory into Claude or Codex homes', () => {
+    const homeDir = createTempDir('install-apply-home-');
+    const projectDir = createTempDir('install-apply-project-');
+
+    try {
+      const claudeResult = run(['--profile', 'core', '--enable-hooks'], { cwd: projectDir, homeDir });
+      assert.strictEqual(claudeResult.code, 0, claudeResult.stderr);
+
+      const claudeRoot = path.join(homeDir, '.claude');
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'agents', 'architect.md')));
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'tdd-workflow', 'SKILL.md')));
+      assert.ok(
+        !fs.existsSync(path.join(claudeRoot, '.agents')),
+        'Claude home must not receive the repo .agents staging directory'
+      );
+
+      const claudeState = readJson(path.join(claudeRoot, 'ecc', 'install-state.json'));
+      assert.ok(
+        !claudeState.operations.some(operation => (
+          String(operation.sourceRelativePath || '').replace(/\\/g, '/').split('/')[0] === '.agents'
+        )),
+        'Claude install-state must not record .agents copy operations'
+      );
+
+      const codexResult = run(['--target', 'codex', '--profile', 'core'], { cwd: projectDir, homeDir });
+      assert.strictEqual(codexResult.code, 0, codexResult.stderr);
+
+      const codexRoot = path.join(homeDir, '.codex');
+      assert.ok(fs.existsSync(path.join(codexRoot, 'agents', 'architect.md')));
+      assert.ok(fs.existsSync(path.join(codexRoot, 'skills', 'tdd-workflow', 'SKILL.md')));
+      assert.ok(
+        !fs.existsSync(path.join(codexRoot, '.agents')),
+        'Codex home must not receive the repo .agents staging directory'
+      );
+
+      const codexState = readJson(path.join(codexRoot, 'ecc-install-state.json'));
+      assert.ok(
+        !codexState.operations.some(operation => (
+          String(operation.sourceRelativePath || '').replace(/\\/g, '/').split('/')[0] === '.agents'
+        )),
+        'Codex install-state must not record .agents copy operations'
+      );
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectDir);
+    }
+  })) passed++; else failed++;
+
   if (test('preserves existing top-level Claude rules and skills during managed install', () => {
     const homeDir = createTempDir('install-apply-home-');
     const projectDir = createTempDir('install-apply-project-');