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_saved_repositories.py

@@ -207,6 +207,23 @@ class TestSaveFailureRollback:
         # Disk still has the entry too — memory and disk stay in sync.
         assert len(json.loads(path.read_text())) == 1
 
+    def test_failed_write_leaves_existing_file_intact(self, tmp_path, monkeypatch):
+        # The save is atomic (temp file + os.replace): a write that dies
+        # mid-serialization must neither truncate the existing file nor
+        # leave a stray .tmp behind.
+        path = tmp_path / "repos.json"
+        manager = make_manager(path)
+        manager.add("https://github.com/user/repo")  # real save
+        before = path.read_text()
+
+        def boom(*args, **kwargs):
+            raise OSError("disk full")
+        monkeypatch.setattr(json, "dump", boom)
+        assert manager.add("https://github.com/user/other") is False
+
+        assert path.read_text() == before
+        assert list(tmp_path.glob("*.tmp")) == []
+
 
 class TestGetAllCopy:
     def test_get_all_is_shallow_copy(self, tmp_path):