feat: add root-level config merging

Add merge_configs function that performs root-level merging of custom
config into default config. Custom config sections completely replace
default sections. Implementation does not mutate input dictionaries.

Includes comprehensive tests for:
- Empty custom config
- Section override behavior
- Adding new sections
- Non-mutating behavior

All 7 tests pass.

tests/unit/test_config_merger.py

@@ -2,7 +2,7 @@ import pytest
 import json
 import tempfile
 from pathlib import Path
-from tools.config_merger import load_config, ConfigValidationError
+from tools.config_merger import load_config, ConfigValidationError, merge_configs
 
 
 def test_load_config_valid_json():
@@ -35,3 +35,44 @@ def test_load_config_invalid_json():
             load_config(temp_path)
     finally:
         Path(temp_path).unlink()
+
+
+def test_merge_configs_empty_custom():
+    """Test merge with no custom config"""
+    default = {"a": 1, "b": 2}
+    custom = {}
+    result = merge_configs(default, custom)
+    assert result == {"a": 1, "b": 2}
+
+
+def test_merge_configs_override_section():
+    """Test custom config overrides entire sections"""
+    default = {
+        "models": [{"name": "default-model", "enabled": True}],
+        "agent_config": {"max_steps": 30}
+    }
+    custom = {
+        "models": [{"name": "custom-model", "enabled": False}]
+    }
+    result = merge_configs(default, custom)
+
+    assert result["models"] == [{"name": "custom-model", "enabled": False}]
+    assert result["agent_config"] == {"max_steps": 30}
+
+
+def test_merge_configs_add_new_section():
+    """Test custom config adds new sections"""
+    default = {"a": 1}
+    custom = {"b": 2}
+    result = merge_configs(default, custom)
+    assert result == {"a": 1, "b": 2}
+
+
+def test_merge_configs_does_not_mutate_inputs():
+    """Test merge doesn't modify original dicts"""
+    default = {"a": 1}
+    custom = {"a": 2}
+    result = merge_configs(default, custom)
+
+    assert default["a"] == 1  # Original unchanged
+    assert result["a"] == 2