fix: address CodeQL alert and review findings

- config_manager: the "secrets list longer than config list" warning now
  interpolates only config-side data (no key name or secrets-derived
  values), resolving the CodeQL clear-text-logging alert.
- base_plugin: validate_config rejects bool display_duration, matching
  get_display_duration (bool is an int subclass and would otherwise pass
  as a positive number).
- config_helper: merge_configs deep-copies override values in the
  non-recursive branch so mutating the merged result cannot reach back
  into override_config.
- saved_repositories: saves are atomic (temp file + fsync + os.replace),
  so a failed write can no longer truncate saved_repositories.json.
- tests: regression cases for each fix, plus a pin that whole-item
  array secrets (key[] + key[].field both marked) strip to empty {}
  skeletons — no secret values can reach config.json.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NohXi78cwsAKtN1sCfxjUh

test/test_config_helper.py

@@ -139,6 +139,16 @@ class TestMergeConfigs:
         assert base == {'a': {'b': 1}}
         assert override == {'a': {'c': 2}}
 
+    def test_no_aliasing_of_override_values(self, helper):
+        # The non-recursive branch must deep-copy the override value too:
+        # mutating a merged-in list or dict must not reach back into
+        # override_config.
+        override = {'teams': ['A', 'B'], 'nested': {'x': [1]}}
+        merged = helper.merge_configs({}, override)
+        merged['teams'].append('C')
+        merged['nested']['x'].append(2)
+        assert override == {'teams': ['A', 'B'], 'nested': {'x': [1]}}
+
 
 class TestValidateConfig:
     def test_no_schema_dict_is_valid(self, helper):