fix: call model configure after Agent mutations

Co-authored-by: Nels <[email protected]>

python/ngen_cal/src/ngen/cal/__main__.py

@@ -57,6 +57,9 @@ def main(general: General, model_conf: Mapping[str, Any]):
 
     # setup plugins
     plugin_manager.hook.ngen_cal_configure(config=general)
+    # Initialize the starting agent
+    # WARNING: Agent sets the model workdir, so initialize it before using the model object for anything that may require an accurate workdir
+    agent = Agent(model, general.workdir, general.log, general.restart, general.strategy.parameters)
     model_inner._plugin_manager.hook.ngen_cal_model_configure(config=model_inner)
 
     print("Starting calib")