fix: --config flag now fully overrides ~/.strix/cli-config.json (#457)

* fix: --config flag now fully overrides ~/.strix/cli-config.json (fixes #377)

Previously, env vars applied from the default config at module import time
were not cleared when --config was later processed, causing settings from
~/.strix/cli-config.json to leak into runs that specified a custom config.

Track which vars were applied by the initial default-config load in
Config._applied_from_default. In apply_config_override, clear those vars
before applying the custom config so only the custom file's settings take effect.

* Add config override regression test

* Make config override test setup explicit

---------

Co-authored-by: octo-patch <octo-patch@github.com>
Co-authored-by: bearsyankees <bearsyankees@gmail.com>

tests/config/test_config_override.py

@@ -0,0 +1,31 @@
+import json
+import os
+
+from strix.config.config import Config, apply_saved_config
+
+
+def test_apply_config_override_clears_default_only_vars(monkeypatch, tmp_path) -> None:
+    from strix.interface.main import apply_config_override
+
+    default_cfg = tmp_path / "cli-config.json"
+    default_cfg.write_text(
+        json.dumps({"env": {"LLM_API_BASE": "https://default.api", "STRIX_LLM": "default-model"}}),
+        encoding="utf-8",
+    )
+    custom_cfg = tmp_path / "custom.json"
+    custom_cfg.write_text(json.dumps({"env": {"STRIX_LLM": "custom-model"}}), encoding="utf-8")
+
+    monkeypatch.setattr(Config, "_config_file_override", None)
+    monkeypatch.setattr(Config, "_applied_from_default", {})
+    monkeypatch.setattr(Config, "config_dir", classmethod(lambda cls: tmp_path))
+    for var_name in Config._llm_env_vars():
+        monkeypatch.delenv(var_name, raising=False)
+
+    apply_saved_config()
+
+    assert os.environ.get("LLM_API_BASE") == "https://default.api"
+
+    apply_config_override(str(custom_cfg))
+
+    assert os.environ.get("STRIX_LLM") == "custom-model"
+    assert "LLM_API_BASE" not in os.environ