core/config: re-read [skills] on reload

`ConfigStore.reload()` re-parsed every section except `[skills]`, so
`/model --persist` and any other in-place reload kept serving the skill config
the process started with — including `[skills].enabled`, which is what decides
whether the skill tools exist at all.

src/plyngent/config/store.py

@@ -494,6 +494,7 @@ class ConfigStore:
         self._plugins = _parse_plugins(cast("dict[str, object]", raw.get("plugins", {})))
         self._networking = _parse_networking(cast("dict[str, object]", raw.get("networking", {})))
         self._mcp = _parse_mcp(cast("dict[str, object]", raw.get("mcp", {})))
+        self._skills = _parse_skills(cast("dict[str, object]", raw.get("skills", {})))
         self._notify = _parse_notify(cast("dict[str, object]", raw.get("notify", {})))
         self._trash = _parse_trash(cast("dict[str, object]", raw.get("trash", {})))
         self._providers, self._bad_providers, self._recoverable_providers = _parse_providers(self._document)

tests/test_config/test_skills_section.py

@@ -40,6 +40,17 @@ allow_write = true
     assert cfg.allow_write is True
 
 
+def test_skills_section_survives_reload(tmp_path: Path) -> None:
+    path = tmp_path / "c.toml"
+    _ = path.write_text('[skills]\npaths = ["~/a"]\n', encoding="utf-8")
+    store = load(path)
+    assert store.skills_config.paths == ["~/a"]
+    _ = path.write_text("[skills]\nenabled = false\npaths = []\n", encoding="utf-8")
+    store.reload()
+    assert store.skills_config.enabled is False
+    assert store.skills_config.paths == []
+
+
 def test_skills_section_invalid_falls_back(tmp_path: Path) -> None:
     """An unknown discovery source or a bad type degrades to the defaults."""
     path = tmp_path / "c.toml"