resolve paths in cli to make config() behavior

Author: Patrick Miles

ScaFFold/cli.py

@@ -181,7 +181,14 @@ def main():
         combined_config["unet_layers"] = (
             combined_config["problem_scale"] - combined_config["unet_bottleneck_dim"] + 1
         )
+
+        # Resolve paths to absolute, matching Config() behavior
+        if "base_run_dir" in combined_config and combined_config["base_run_dir"]:
+            combined_config["base_run_dir"] = str(Path(combined_config["base_run_dir"]).resolve())
 
+        if "dataset_dir" in combined_config and combined_config["dataset_dir"]:
+            combined_config["dataset_dir"] = str(Path(combined_config["dataset_dir"]).resolve())
+            
         # Calculate these variables after override
         combined_config["vol_size"] = pow(2, combined_config["problem_scale"])
         combined_config["point_num"] = int(combined_config["vol_size"] ** 3 / 256)