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/ISC/Tabs/SettingsTab.qml

@@ -225,7 +225,7 @@ Item {
                             Layout.preferredWidth: 90
                             Layout.preferredHeight: Theme.settingsButtonHeight
                             onClicked: {
-                                settingsModel.setChamberId(chamberField.text);
+                                settingsModel.ChamberId = chamberField.text;
                                 settingsModel.saveSettings();
                             }
                         }
@@ -296,7 +296,7 @@ Item {
                         SettingsToggle {
                             text: "Reverse Z Wafer"
                             checked: settingsModel.reverseZWafer
-                            onToggled: settingsModel.setReverseZWafer(checked)
+                            onToggled: settingsModel.reverseZWafer = checked
                         }
                     }
                 }