fix(web): auto_update and other core settings are not orphaned plugins (#589)

v3.4.0 shows "Plugin Config Warning - In config but not installed:
auto_update. Reinstall via the Plugin Store, or remove these entries from
config.json." auto_update is the core weekly-update setting from #581.
Reconciliation treated every top-level dict not in its private
_SYSTEM_CONFIG_KEYS list as a plugin id, and #581 could not know to extend
that list.

- Move core top-level keys into src/core_config_keys.py (CORE_CONFIG_KEYS)
  and use it in reconciliation. Tests fail if a config.template.json key or
  a key written by the general-settings save is missing from it.
- A secrets-file key only counts as a non-plugin when no installed plugin
  has that id. Plugin secrets are namespaced by id, so installed plugins
  with secrets were reported as missing from config on every run.
- still_unresolved() drops "not on disk" findings whose id is no longer a
  plugin entry in config, so a stored verdict clears without a restart.
- A plugin whose id is a core key is skipped with a warning, and the fix
  never writes a plugin stub over or in place of a core setting.

Co-authored-by: Claude Opus 5 <noreply@anthropic.com>

web_interface/blueprints/api_v3/plugins.py

@@ -735,10 +735,10 @@ def _drop_stale_reconciliation_findings(unresolved):
         )
 
         cm = api_v3.config_manager
-        config_keys = config_plugin_ids(cm.load_config() or {},
-                                       ignored_config_keys(cm))
         plugins_dir = getattr(api_v3.plugin_manager, 'plugins_dir', None)
         installed = disk_plugin_ids(plugins_dir) if plugins_dir else set()
+        config_keys = config_plugin_ids(cm.load_config() or {},
+                                       ignored_config_keys(cm, installed))
         return still_unresolved(unresolved, config_keys, installed)
     except Exception:
         logger.debug("[Reconciliation] Could not re-check stored findings", exc_info=True)