refactor: prune orphaned attic modules and standardize project configurations

- Move orphaned modules (data_segment.py, contour_models.py, marching_squares.py) to attic/.
- Standardize local settings logic, serial port parameters, and graph view plots.
- Update pyproject.toml pyside6-project dependencies and configure gitignore.

src/pygui/backend/data/local_settings.py

@@ -1,7 +1,10 @@
 import json
+import logging
 import os
 from pathlib import Path
 
+log = logging.getLogger(__name__)
+
 
 # ===== Settings Persistence Model =====
 class LocalSettings:
@@ -51,7 +54,8 @@ class LocalSettings:
                 if hasattr(settings, key):
                     setattr(settings, key, value)
         except Exception as e:
-            print(f"Error reading setting file: {e}")
+            log = logging.getLogger(__name__)
+            log.warning("Error reading setting file: %s",e)
 
         return settings
 
@@ -66,7 +70,7 @@ class LocalSettings:
             with open(path, "w", encoding="utf-8") as f:
                 json.dump(data, f, indent=4)
         except Exception as e:
-            print(f"Error saving settings: {e}")
+            log.exception("Error saving settings: %s",e)
 
     # ===== Master File Helpers =====
     @classmethod