fix(install): keep foreign Claude hooks in mixed groups

Remove only setup-owned hook entries from a hook group and keep foreign
entries with their group options, such as matcher.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

scripts/lib/install-options.py

@@ -73,18 +73,23 @@ def merge_json(current, managed):
                 groups = value.get(event, [])
                 old_groups = hooks.get(event, [])
                 if isinstance(groups, list) and isinstance(old_groups, list):
-                    retained = [group for group in old_groups if not any(
+                    retained = []
-                        re.search(r'(?:flashbang|statusline|record-compact|session-state-pointer)\.(?:ps1|sh)',
+                    for group in old_groups:
-                                  str(hook.get('command', '')) + str(hook.get('command_windows', '')), re.I)
+                        if not isinstance(group, dict) or not isinstance(group.get('hooks'), list):
-                        for hook in group.get('hooks', []) if isinstance(hook, dict)
+                            retained.append(group)
-                    )]
+                            continue
+                        foreign = [hook for hook in group['hooks'] if not (isinstance(hook, dict) and re.search(
+                            r'(?:flashbang|statusline|record-compact|session-state-pointer)\.(?:ps1|sh)',
+                            str(hook.get('command', '')) + str(hook.get('command_windows', '')), re.I))]
+                        if foreign:
+                            retained.append(dict(group, hooks=foreign))
                     merged = groups + [group for group in retained if group not in groups]
                     if merged:
                         hooks[event] = merged
                     else:
                         hooks.pop(event, None)
                 else:
-                    hooks[event] = value
+                    hooks[event] = groups
             result[key] = hooks
         elif isinstance(value, dict) and isinstance(result.get(key), dict):
             result[key] = merge_json(result[key], value)

scripts/tests/test-install-options.py

@@ -45,6 +45,19 @@ class InstallOptionsTests(unittest.TestCase):
         self.assertEqual(result['mcp_servers'], {'demo': {'command': 'demo', 'env': {'TOKEN_NAME': 'x'}}})
         self.assertEqual(result['model_providers'], {'custom': {'name': 'Custom', 'base_url': 'https://example.invalid'}})
 
+    def test_merge_json_removes_only_owned_hooks_from_mixed_group(self):
+        owned = {'type': 'command', 'command': 'bash "/old/hooks/flashbang.sh"', 'timeout': 8}
+        foreign = {'type': 'command', 'command': 'notify-done', 'timeout': 3}
+        current = {'hooks': {'Stop': [{'matcher': 'custom', 'hooks': [owned, foreign]}],
+                             'PreCompact': [{'hooks': [{'type': 'command', 'command': 'bash "/old/record-compact.sh"'}]}]}}
+        managed_stop = {'hooks': [{'type': 'command', 'command': 'bash "/new/hooks/flashbang.sh"', 'timeout': 8}]}
+        managed = {'hooks': {'Stop': [managed_stop], 'PreCompact': []}}
+
+        hooks = OPTIONS.merge_json(current, managed)['hooks']
+
+        self.assertEqual(hooks['Stop'], [managed_stop, {'matcher': 'custom', 'hooks': [foreign]}])
+        self.assertNotIn('PreCompact', hooks)
+
     def test_merge_cli_accepts_bom_input_and_preserves_non_ascii(self):
         with tempfile.TemporaryDirectory() as directory:
             current = Path(directory) / 'config.toml'