feat: Implement application preferences with JSON persistence

- Added preferences management in `preferences.py` with functions to load, save, get, set, and reset preferences.
- Introduced a configuration directory structure based on the operating system.
- Integrated preferences into the settings window, allowing users to reset settings and manage window geometry.
- Enhanced `search_filter.py` to support flexible date column names and improved filtering logic.
- Updated `settings_window.py` to include options for managing backup and configuration folder paths.
- Introduced an `UndoManager` class to handle undo actions for add/update/delete operations.
- Improved UIManager to support sorting in tree views and added a toast notification feature.

src/main.py

@@ -1,8 +1,10 @@
+import contextlib
 import os
 import sys
 import tkinter as tk
 from collections.abc import Callable
-from tkinter import messagebox, ttk
+from datetime import datetime
+from tkinter import filedialog, messagebox, ttk
 from typing import Any
 
 import pandas as pd
@@ -20,11 +22,13 @@ from medicine_management_window import MedicineManagementWindow
 from medicine_manager import MedicineManager
 from pathology_management_window import PathologyManagementWindow
 from pathology_manager import PathologyManager
+from preferences import get_config_dir, get_pref, save_preferences, set_pref
 from search_filter import DataFilter
 from search_filter_ui import SearchFilterWidget
 from settings_window import SettingsWindow
 from theme_manager import ThemeManager
 from ui_manager import UIManager
+from undo_manager import UndoAction, UndoManager
 
 
 class MedTrackerApp:
@@ -34,19 +38,23 @@ class MedTrackerApp:
         self.root.title("Thechart - medication tracker")
         self.root.protocol("WM_DELETE_WINDOW", self.handle_window_closing)
 
+        # Live geometry persistence state
+        self._geom_save_job: str | None = None
+        self._last_saved_geometry: str = ""
+
         # Set up data file
         self.filename: str = "thechart_data.csv"
         first_argument: str = ""
-
         if len(sys.argv) > 1:
-            first_argument: str = sys.argv[1]
+            first_argument = sys.argv[1]
             if os.path.exists(first_argument):
                 self.filename = first_argument
                 logger.info(f"Using data file: {first_argument}")
             else:
                 logger.warning(
-                    f"Data file {first_argument} doesn't exist. \
-                    Using default file: {self.filename}"
+                    "Data file %s doesn't exist. Using default file: %s",
+                    first_argument,
+                    self.filename,
                 )
 
         logger.info(f"Log level: {LOG_LEVEL}")
@@ -73,6 +81,8 @@ class MedTrackerApp:
             self.pathology_manager,
             self.theme_manager,
         )
+        # Undo manager (history of data mutations)
+        self.undo_manager: UndoManager = UndoManager()
 
         # Update error handler with UI manager for user feedback
         self.error_handler.ui_manager = self.ui_manager
@@ -90,7 +100,11 @@ class MedTrackerApp:
         self.auto_save_manager = AutoSaveManager(
             save_callback=self._auto_save_callback, interval_minutes=5, logger=logger
         )
-        self.backup_manager = BackupManager(data_file_path=self.filename, logger=logger)
+        self.backup_manager = BackupManager(
+            data_file_path=self.filename,
+            logger=logger,
+            status_callback=self._on_backup_status,
+        )
 
         # Initialize search/filter system
         self.data_filter = DataFilter()
@@ -106,8 +120,26 @@ class MedTrackerApp:
         # Setup keyboard shortcuts
         self._setup_keyboard_shortcuts()
 
-        # Center the window on screen
-        self._center_window()
+        # Apply window preferences (geometry, always-on-top) then center if needed
+        with contextlib.suppress(Exception):
+            self.root.wm_attributes("-topmost", bool(get_pref("always_on_top", False)))
+
+        geom = str(get_pref("last_window_geometry", ""))
+        if get_pref("remember_window_geometry", True) and geom:
+            try:
+                self.root.geometry(geom)
+            except Exception:
+                self._center_window()
+        else:
+            # Center the window on screen
+            self._center_window()
+
+        # Bind configure to persist geometry live (debounced)
+        try:
+            self.root.bind("<Configure>", self._on_configure, add="+")
+        except Exception:
+            # Older Tk variants may not support add; fall back
+            self.root.bind("<Configure>", self._on_configure)
 
         # Enable auto-save by default
         self.auto_save_manager.enable_auto_save()
@@ -115,6 +147,143 @@ class MedTrackerApp:
         # Create initial backup
         self.backup_manager.create_backup("startup")
 
+    def _on_configure(self, _event: object | None = None) -> None:
+        """Debounce window configure events to persist geometry live."""
+        # Skip when user disabled remembering geometry
+        with contextlib.suppress(Exception):
+            if not get_pref("remember_window_geometry", True):
+                return
+
+        # Avoid saving while minimized
+        with contextlib.suppress(Exception):
+            if getattr(self.root, "state", lambda: "normal")() == "iconic":
+                return
+
+        # Debounce saves to limit disk writes
+        if self._geom_save_job is not None:
+            with contextlib.suppress(Exception):
+                self.root.after_cancel(self._geom_save_job)
+            self._geom_save_job = None
+
+        with contextlib.suppress(Exception):
+            self._geom_save_job = self.root.after(600, self._save_geometry_now)
+
+    def _save_geometry_now(self) -> None:
+        """Capture current geometry and persist to preferences if changed."""
+        try:
+            geom = self.root.geometry()
+            if geom and geom != self._last_saved_geometry:
+                set_pref("last_window_geometry", geom)
+                save_preferences()
+                self._last_saved_geometry = geom
+        except Exception:
+            pass
+
+    def _on_backup_status(self, msg: str) -> None:
+        """Handle backup-related status updates with status bar and toast."""
+        try:
+            self.ui_manager.update_status(msg, "success")
+            # Show a brief toast for backup events if available
+            if hasattr(self.ui_manager, "show_toast"):
+                # Keep toast short to avoid annoyance during startup/shutdown
+                self.ui_manager.show_toast(msg, 1500)
+            # Update 'Last backup' indicator on backup creation
+            if "Backup created:" in msg and hasattr(
+                self.ui_manager, "update_last_backup"
+            ):
+                when = datetime.now().strftime("%Y-%m-%d %H:%M")
+                self.ui_manager.update_last_backup(when)
+        except Exception as exc:
+            logger.error(f"Failed to show backup status: {exc}")
+
+    def _restore_from_backup(self) -> None:
+        """Prompt user to select a backup CSV and restore it."""
+        initial_dir = getattr(self.backup_manager, "backup_directory", os.getcwd())
+        file_path = filedialog.askopenfilename(
+            parent=self.root,
+            title="Restore from Backup",
+            initialdir=initial_dir,
+            filetypes=[("CSV Files", "*.csv"), ("All Files", "*.*")],
+        )
+        if not file_path:
+            return
+        # Build a detailed confirmation with file info
+        try:
+            size_b = os.path.getsize(file_path)
+
+            def _fmt_size(n: int) -> str:
+                for unit in ["B", "KB", "MB", "GB"]:
+                    if n < 1024:
+                        return f"{n:.1f} {unit}" if unit != "B" else f"{n} B"
+                    n /= 1024
+                return f"{n:.1f} TB"
+
+            mtime = datetime.fromtimestamp(os.path.getmtime(file_path))
+            mtime_str = mtime.strftime("%Y-%m-%d %H:%M")
+            confirm_msg = (
+                "You're about to restore data from this backup file:\n\n"
+                f"• File: {os.path.basename(file_path)}\n"
+                f"• Size: {_fmt_size(size_b)}\n"
+                f"• Modified: {mtime_str}\n\n"
+                f"This will replace: {os.path.abspath(self.filename)}\n\n"
+                "A pre-restore backup of the current data will be created.\n\n"
+                "Proceed with restore?"
+            )
+        except Exception:
+            confirm_msg = "Restore selected backup? Current data will be saved first."
+
+        if not messagebox.askyesno("Confirm Restore", confirm_msg, parent=self.root):
+            return
+        try:
+            # Create a safety backup of the current data before restoring
+            try:
+                self.backup_manager.create_backup("pre_restore")
+            except Exception as _exc:
+                logger.warning(f"Pre-restore backup failed: {_exc}")
+
+            ok = self.backup_manager.restore_from_backup(file_path)
+            if ok:
+                if hasattr(self.data_manager, "_invalidate_cache"):
+                    self.data_manager._invalidate_cache()
+                self.refresh_data_display()
+                base = os.path.basename(file_path)
+                self.ui_manager.update_status(f"Restored from: {base}", "success")
+                if hasattr(self.ui_manager, "show_toast"):
+                    self.ui_manager.show_toast(f"Restored: {base}", 1800)
+
+                # Offer to open the folder containing the restored file (if opted-in)
+                try:
+                    if get_pref(
+                        "prompt_open_folder_after_restore", False
+                    ) and messagebox.askyesno(
+                        "Restore Complete",
+                        (
+                            f"Restored from '{base}'.\n\n"
+                            "Open the containing backups folder now?"
+                        ),
+                        parent=self.root,
+                    ):
+                        path = os.path.dirname(file_path)
+                        if sys.platform.startswith("darwin"):
+                            os.system(f'open "{path}"')
+                        elif os.name == "nt":
+                            os.startfile(path)  # type: ignore[attr-defined]
+                        else:
+                            os.system(f'xdg-open "{path}" >/dev/null 2>&1 &')
+                except Exception as _e:
+                    logger.warning(f"Failed to open restored folder: {_e}")
+            else:
+                self.ui_manager.update_status("Restore failed", "error")
+                messagebox.showerror(
+                    "Restore Failed",
+                    "Could not restore backup.",
+                    parent=self.root,
+                )
+        except Exception as e:
+            logger.error(f"Restore from backup failed: {e}")
+            self.ui_manager.update_status("Restore failed", "error")
+            messagebox.showerror("Restore Failed", str(e), parent=self.root)
+
     def _center_window(self) -> None:
         """Center the main window on the screen."""
         # Update the window to get accurate dimensions
@@ -226,41 +395,79 @@ class MedTrackerApp:
         file_menu = self.theme_manager.create_themed_menu(menubar, tearoff=0)
         menubar.add_cascade(label="File", menu=file_menu)
         file_menu.add_command(
-            label="Export Data...",
+            label="Export Data... (Ctrl+E)",
             command=self._open_export_window,
             accelerator="Ctrl+E",
         )
         file_menu.add_separator()
         file_menu.add_command(
-            label="Exit", command=self.handle_window_closing, accelerator="Ctrl+Q"
+            label="Exit (Ctrl+Q)",
+            command=self.handle_window_closing,
+            accelerator="Ctrl+Q",
         )
 
         # Tools menu
         tools_menu = self.theme_manager.create_themed_menu(menubar, tearoff=0)
         menubar.add_cascade(label="Tools", menu=tools_menu)
         tools_menu.add_command(
-            label="Manage Pathologies...",
+            label="Manage Pathologies... (Ctrl+P)",
             command=self._open_pathology_manager,
             accelerator="Ctrl+P",
         )
         tools_menu.add_command(
-            label="Manage Medicines...",
+            label="Manage Medicines... (Ctrl+M)",
             command=self._open_medicine_manager,
             accelerator="Ctrl+M",
         )
         tools_menu.add_separator()
         tools_menu.add_command(
-            label="Clear Entries", command=self._clear_entries, accelerator="Ctrl+N"
+            label="Clear Entries (Ctrl+N)",
+            command=self._clear_entries,
+            accelerator="Ctrl+N",
         )
         tools_menu.add_command(
-            label="Refresh Data", command=self.refresh_data_display, accelerator="F5"
+            label="Refresh Data (F5)",
+            command=self.refresh_data_display,
+            accelerator="F5",
         )
         tools_menu.add_separator()
         tools_menu.add_command(
-            label="Search & Filter",
+            label="Search & Filter (Ctrl+F)",
             command=self._toggle_search_filter,
             accelerator="Ctrl+F",
         )
+        tools_menu.add_separator()
+        tools_menu.add_command(
+            label="Open Logs Folder (Ctrl+L)",
+            command=self._open_logs_folder,
+            accelerator="Ctrl+L",
+        )
+        tools_menu.add_command(
+            label="Open Data Folder (Ctrl+D)",
+            command=self._open_data_folder,
+            accelerator="Ctrl+D",
+        )
+        tools_menu.add_command(
+            label="Open Backups Folder (Ctrl+B)",
+            command=self._open_backups_folder,
+            accelerator="Ctrl+B",
+        )
+        tools_menu.add_command(
+            label="Create Backup Now (Ctrl+Shift+B)",
+            command=self._create_manual_backup,
+            accelerator="Ctrl+Shift+B",
+        )
+        tools_menu.add_command(
+            label="Restore from Backup... (Ctrl+Shift+R)",
+            command=self._restore_from_backup,
+            accelerator="Ctrl+Shift+R",
+        )
+        tools_menu.add_separator()
+        tools_menu.add_command(
+            label="Open Config Folder (Ctrl+Shift+C)",
+            command=self._open_config_folder,
+            accelerator="Ctrl+Shift+C",
+        )
 
         # Theme menu
         theme_menu = self.theme_manager.create_themed_menu(menubar, tearoff=0)
@@ -279,66 +486,92 @@ class MedTrackerApp:
 
         theme_menu.add_separator()
         theme_menu.add_command(
-            label="More Settings...",
+            label="More Settings... (F2)",
             command=self._open_settings_window,
+            accelerator="F2",
         )
 
         # Help menu
         help_menu = self.theme_manager.create_themed_menu(menubar, tearoff=0)
         menubar.add_cascade(label="Help", menu=help_menu)
         help_menu.add_command(
-            label="Settings...",
-            command=self._open_settings_window,
-            accelerator="F2",
-        )
-        help_menu.add_separator()
-        help_menu.add_command(
-            label="Keyboard Shortcuts",
+            label="Keyboard Shortcuts (F1)",
             command=self._show_keyboard_shortcuts,
             accelerator="F1",
         )
         help_menu.add_command(label="About", command=self._show_about_dialog)
+        help_menu.add_separator()
+        help_menu.add_command(
+            label="Open Documentation (Ctrl+H)",
+            command=self._open_documentation,
+            accelerator="Ctrl+H",
+        )
 
     def _setup_keyboard_shortcuts(self) -> None:
         """Set up keyboard shortcuts for common actions."""
-        # Bind keyboard shortcuts to the main window
-        self.root.bind("<Control-s>", lambda e: self.add_new_entry())
-        self.root.bind("<Control-S>", lambda e: self.add_new_entry())
-        self.root.bind("<Control-q>", lambda e: self.handle_window_closing())
-        self.root.bind("<Control-Q>", lambda e: self.handle_window_closing())
-        self.root.bind("<Control-e>", lambda e: self._open_export_window())
-        self.root.bind("<Control-E>", lambda e: self._open_export_window())
-        self.root.bind("<Control-n>", lambda e: self._clear_entries())
-        self.root.bind("<Control-N>", lambda e: self._clear_entries())
-        self.root.bind("<Control-r>", lambda e: self.refresh_data_display())
-        self.root.bind("<Control-R>", lambda e: self.refresh_data_display())
-        self.root.bind("<F5>", lambda e: self.refresh_data_display())
-        self.root.bind("<Control-m>", lambda e: self._open_medicine_manager())
-        self.root.bind("<Control-M>", lambda e: self._open_medicine_manager())
-        self.root.bind("<Control-p>", lambda e: self._open_pathology_manager())
-        self.root.bind("<Control-P>", lambda e: self._open_pathology_manager())
-        self.root.bind("<Control-f>", lambda e: self._toggle_search_filter())
-        self.root.bind("<Control-F>", lambda e: self._toggle_search_filter())
-        self.root.bind("<Delete>", lambda e: self._delete_selected_entry())
-        self.root.bind("<Escape>", lambda e: self._clear_selection())
-        self.root.bind("<F1>", lambda e: self._show_keyboard_shortcuts())
-        self.root.bind("<F2>", lambda e: self._open_settings_window())
+        bindings = [
+            ("<Control-s>", self.add_new_entry),
+            ("<Control-S>", self.add_new_entry),
+            ("<Control-q>", self.handle_window_closing),
+            ("<Control-Q>", self.handle_window_closing),
+            ("<Control-e>", self._open_export_window),
+            ("<Control-E>", self._open_export_window),
+            ("<Control-n>", self._clear_entries),
+            ("<Control-N>", self._clear_entries),
+            ("<Control-r>", self.refresh_data_display),
+            ("<Control-R>", self.refresh_data_display),
+            ("<F5>", self.refresh_data_display),
+            ("<Control-m>", self._open_medicine_manager),
+            ("<Control-M>", self._open_medicine_manager),
+            ("<Control-p>", self._open_pathology_manager),
+            ("<Control-P>", self._open_pathology_manager),
+            ("<Control-f>", self._toggle_search_filter),
+            ("<Control-F>", self._toggle_search_filter),
+            ("<Delete>", self._delete_selected_entry),
+            ("<Escape>", self._clear_selection),
+            ("<F1>", self._show_keyboard_shortcuts),
+            ("<F2>", self._open_settings_window),
+            ("<Control-z>", self._undo_last),
+            ("<Control-Z>", self._undo_last),
+            ("<Control-l>", self._open_logs_folder),
+            ("<Control-L>", self._open_logs_folder),
+            ("<Control-d>", self._open_data_folder),
+            ("<Control-D>", self._open_data_folder),
+            ("<Control-b>", self._open_backups_folder),
+            ("<Control-B>", self._open_backups_folder),
+            ("<Control-h>", self._open_documentation),
+            ("<Control-H>", self._open_documentation),
+            ("<Control-Shift-B>", self._create_manual_backup),
+            ("<Control-Shift-R>", self._restore_from_backup),
+            ("<Control-Shift-C>", self._open_config_folder),
+        ]
+        for seq, func in bindings:
+            self.root.bind(seq, lambda e, f=func: f())
 
-        # Make the window focusable so it can receive key events
         self.root.focus_set()
-
         logger.info("Keyboard shortcuts configured:")
-        logger.info("  Ctrl+S: Save/Add new entry")
-        logger.info("  Ctrl+Q: Quit application")
-        logger.info("  Ctrl+E: Export data")
-        logger.info("  Ctrl+N: Clear entries")
-        logger.info("  Ctrl+R/F5: Refresh data")
-        logger.info("  Ctrl+M: Manage medicines")
-        logger.info("  Ctrl+P: Manage pathologies")
-        logger.info("  Ctrl+F: Toggle search/filter")
-        logger.info("  Delete: Delete selected entry")
-        logger.info("  Escape: Clear selection")
-        logger.info("  F1: Show keyboard shortcuts help")
+        for desc in [
+            "Ctrl+S: Save/Add new entry",
+            "Ctrl+Q: Quit application",
+            "Ctrl+E: Export data",
+            "Ctrl+N: Clear entries",
+            "Ctrl+R/F5: Refresh data",
+            "Ctrl+M: Manage medicines",
+            "Ctrl+P: Manage pathologies",
+            "Ctrl+F: Toggle search/filter",
+            "Ctrl+L: Open logs folder",
+            "Ctrl+D: Open data folder",
+            "Ctrl+B: Open backups folder",
+            "Ctrl+Shift+B: Create backup now",
+            "Ctrl+Shift+R: Restore from backup...",
+            "Ctrl+Shift+C: Open config folder",
+            "Ctrl+H: Open documentation",
+            "Delete: Delete selected entry",
+            "Escape: Clear selection",
+            "F1: Show keyboard shortcuts help",
+            "Ctrl+Z: Undo last change",
+        ]:
+            logger.info("  " + desc)
 
     def _show_keyboard_shortcuts(self) -> None:
         """Show a dialog with keyboard shortcuts information."""
@@ -353,6 +586,8 @@ Data Management:
 • Ctrl+N: Clear entries
 • Ctrl+R / F5: Refresh data
 • Ctrl+F: Toggle search/filter
+• Ctrl+L: Open logs folder
+• Ctrl+D: Open data folder
 
 Window Management:
 • Ctrl+M: Manage medicines
@@ -362,21 +597,49 @@ Table Operations:
 • Delete: Delete selected entry
 • Escape: Clear selection
 • Double-click: Edit entry
+• Ctrl+Z: Undo last change
 
 Help:
 • F1: Show this help dialog
-• F2: Open settings window"""
+• F2: Open settings window
+• Ctrl+H: Open documentation
+• Ctrl+Shift+B: Create backup now
+• Ctrl+Shift+R: Restore from backup...
+• Ctrl+Shift+C: Open config folder
+"""
 
         messagebox.showinfo("Keyboard Shortcuts", shortcuts_text, parent=self.root)
 
+    def _open_documentation(self) -> None:
+        """Open the docs directory in your default file viewer or README in browser."""
+        # Prefer docs/ directory; else open README.md
+        docs_dir = os.path.join(os.getcwd(), "docs")
+        target = (
+            docs_dir
+            if os.path.isdir(docs_dir)
+            else os.path.join(os.getcwd(), "README.md")
+        )
+        try:
+            if sys.platform.startswith("darwin"):
+                os.system(f'open "{target}"')
+            elif os.name == "nt":
+                os.startfile(target)  # type: ignore[attr-defined]
+            else:
+                os.system(f'xdg-open "{target}" >/dev/null 2>&1 &')
+            self.ui_manager.update_status("Opened documentation", "success")
+            if hasattr(self.ui_manager, "show_toast"):
+                self.ui_manager.show_toast("Documentation opened", 1500)
+        except Exception as e:
+            logger.error(f"Failed to open documentation: {e}")
+            self.ui_manager.update_status("Failed to open documentation", "error")
+
     def _change_theme(self, theme_name: str) -> None:
         """Change the application theme."""
         if self.theme_manager.apply_theme(theme_name):
             self.ui_manager.update_status(
                 f"Theme changed to: {theme_name.title()}", "info"
             )
-            # Refresh the menu to update radio button selection
-            self._setup_menu()
+            self._setup_menu()  # Refresh menu radio selection
         else:
             self.ui_manager.update_status(
                 f"Failed to apply theme: {theme_name}", "error"
@@ -402,6 +665,8 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
         """Open the export window."""
         self.ui_manager.update_status("Opening export window", "info")
         ExportWindow(self.root, self.export_manager)
+        if hasattr(self.ui_manager, "show_toast"):
+            self.ui_manager.show_toast("Export window opened", 1200)
 
     def _open_pathology_manager(self) -> None:
         """Open the pathology management window."""
@@ -417,10 +682,106 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
             self.root, self.medicine_manager, self._refresh_ui_after_config_change
         )
 
+    def _open_logs_folder(self) -> None:
+        """Open the application logs directory in the system file explorer."""
+        path = LOG_PATH
+        try:
+            if not os.path.exists(path):
+                os.makedirs(path, exist_ok=True)
+            # Cross-platform opener
+            if sys.platform.startswith("darwin"):
+                os.system(f'open "{path}"')
+            elif os.name == "nt":
+                os.startfile(path)  # type: ignore[attr-defined]
+            else:
+                # Linux
+                os.system(f'xdg-open "{path}" >/dev/null 2>&1 &')
+            self.ui_manager.update_status("Opened logs folder", "success")
+            if hasattr(self.ui_manager, "show_toast"):
+                self.ui_manager.show_toast("Logs folder opened", 1500)
+        except Exception as e:
+            logger.error(f"Failed to open logs folder: {e}")
+            self.ui_manager.update_status("Failed to open logs folder", "error")
+
+    def _open_data_folder(self) -> None:
+        """Open the data file's directory in the system file explorer."""
+        try:
+            folder = os.path.dirname(os.path.abspath(self.filename)) or "."
+            if not os.path.exists(folder):
+                os.makedirs(folder, exist_ok=True)
+            if sys.platform.startswith("darwin"):
+                os.system(f'open "{folder}"')
+            elif os.name == "nt":
+                os.startfile(folder)  # type: ignore[attr-defined]
+            else:
+                os.system(f'xdg-open "{folder}" >/dev/null 2>&1 &')
+            self.ui_manager.update_status("Opened data folder", "success")
+            if hasattr(self.ui_manager, "show_toast"):
+                self.ui_manager.show_toast("Data folder opened", 1500)
+        except Exception as e:
+            logger.error(f"Failed to open data folder: {e}")
+            self.ui_manager.update_status("Failed to open data folder", "error")
+
     def _open_settings_window(self) -> None:
         """Open the settings window."""
         self.ui_manager.update_status("Opening settings window", "info")
         SettingsWindow(self.root, self.theme_manager, self.ui_manager)
+        if hasattr(self.ui_manager, "show_toast"):
+            self.ui_manager.show_toast("Settings opened", 1200)
+
+    def _open_config_folder(self) -> None:
+        """Open the application configuration folder in the file explorer."""
+        try:
+            path = get_config_dir()
+            if not os.path.exists(path):
+                os.makedirs(path, exist_ok=True)
+            if sys.platform.startswith("darwin"):
+                os.system(f'open "{path}"')
+            elif os.name == "nt":
+                os.startfile(path)  # type: ignore[attr-defined]
+            else:
+                os.system(f'xdg-open "{path}" >/dev/null 2>&1 &')
+            self.ui_manager.update_status("Opened config folder", "success")
+            if hasattr(self.ui_manager, "show_toast"):
+                self.ui_manager.show_toast("Config folder opened", 1500)
+        except Exception as e:
+            logger.error(f"Failed to open config folder: {e}")
+            self.ui_manager.update_status("Failed to open config folder", "error")
+
+    def _create_manual_backup(self) -> None:
+        """Create a manual backup immediately."""
+        try:
+            self.ui_manager.update_status("Creating backup...", "info")
+            self.backup_manager.create_backup("manual")
+            # Optional cleanup to enforce retention policy
+            if hasattr(self.backup_manager, "cleanup_old_backups"):
+                self.backup_manager.cleanup_old_backups(keep_count=5)
+        except Exception as e:
+            logger.error(f"Manual backup failed: {e}")
+            self.ui_manager.update_status("Manual backup failed", "error")
+
+    def _open_backups_folder(self) -> None:
+        """Open the backups directory in the system file explorer."""
+        # Prefer the manager's directory if available
+        path = getattr(self.backup_manager, "backup_directory", None)
+        if not path:
+            # Fallback to data file's directory
+            path = os.path.dirname(os.path.abspath(self.filename)) or "."
+        try:
+            if not os.path.exists(path):
+                os.makedirs(path, exist_ok=True)
+            if sys.platform.startswith("darwin"):
+                os.system(f'open "{path}"')
+            elif os.name == "nt":
+                os.startfile(path)  # type: ignore[attr-defined]
+            else:
+                os.system(f'xdg-open "{path}" >/dev/null 2>&1 &')
+            self.ui_manager.update_status("Opened backups folder", "success")
+            if hasattr(self.ui_manager, "show_toast"):
+                self.ui_manager.show_toast("Backups folder opened", 1500)
+        except Exception as e:
+            logger.error(f"Failed to open backups folder: {e}")
+            self.ui_manager.update_status("Failed to open backups folder", "error")
 
     def _refresh_ui_after_config_change(self) -> None:
         """Refresh UI components after pathology or medicine configuration changes."""
@@ -430,9 +791,15 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
 
         # Clear caches in optimized data manager
         if hasattr(self.data_manager, "_invalidate_cache"):
-            self.data_manager._invalidate_cache()
-            self.data_manager._headers_cache = None
-            self.data_manager._dtype_cache = None
+            # Use public structural invalidation method if available
+            if hasattr(self.data_manager, "invalidate_structure"):
+                self.data_manager.invalidate_structure()
+            else:
+                self.data_manager._invalidate_cache()
+                if hasattr(self.data_manager, "_headers_cache"):
+                    self.data_manager._headers_cache = None
+                if hasattr(self.data_manager, "_dtype_cache"):
+                    self.data_manager._dtype_cache = None
 
         # Recreate the input frame with new pathologies and medicines
         self.input_frame.destroy()
@@ -488,7 +855,8 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
         ):
             date: str = item_values[0]
             logger.debug(f"Deleting entry with date={date}")
-
+            # Capture row BEFORE deletion for undo
+            deleted_row = self.data_manager.get_row(date)
             self.ui_manager.update_status("Deleting entry...", "info")
             if self.data_manager.delete_entry(date):
                 self._mark_data_modified()  # Mark for auto-save
@@ -497,6 +865,25 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
                     "Success", "Entry deleted successfully!", parent=self.root
                 )
                 self.refresh_data_display()
+                if deleted_row:
+
+                    def _undo_del() -> None:
+                        import csv as _csv
+
+                        existing = self.data_manager.load_data()
+                        if (
+                            not existing.empty
+                            and "date" in existing.columns
+                            and date in existing["date"].values
+                        ):
+                            return  # Already restored
+                        with open(self.filename, "a", newline="") as _f:
+                            _csv.writer(_f).writerow(deleted_row)
+                        if hasattr(self.data_manager, "_invalidate_cache"):
+                            self.data_manager._invalidate_cache()
+                        self.refresh_data_display()
+
+                    self.undo_manager.push(UndoAction(f"Delete {date}", _undo_del))
             else:
                 self.ui_manager.update_status("Failed to delete entry", "error")
                 messagebox.showerror(
@@ -624,6 +1011,8 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
         values.append(note)
 
         self.ui_manager.update_status("Saving changes...", "info")
+        # Capture previous row BEFORE updating
+        prev_row = self.data_manager.get_row(original_date)
         if self.data_manager.update_entry(original_date, values):
             self._mark_data_modified()  # Mark for auto-save
             edit_win.destroy()
@@ -633,6 +1022,22 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
             )
             self._clear_entries()
             self.refresh_data_display()
+            new_date = values[0]
+
+            def _undo_update() -> None:
+                import csv as _csv
+
+                # Remove the updated (new) row
+                self.data_manager.delete_entry(str(new_date))
+                # Restore previous row
+                if prev_row:
+                    with open(self.filename, "a", newline="") as _f:
+                        _csv.writer(_f).writerow(prev_row)
+                if hasattr(self.data_manager, "_invalidate_cache"):
+                    self.data_manager._invalidate_cache()
+                self.refresh_data_display()
+
+            self.undo_manager.push(UndoAction(f"Update {original_date}", _undo_update))
         else:
             # Check if it's a duplicate date issue
             df = self.data_manager.load_data()
@@ -653,6 +1058,11 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
         if messagebox.askokcancel(
             "Quit", "Do you want to quit the application?", parent=self.root
         ):
+            # Save window geometry if preference is enabled
+            with contextlib.suppress(Exception):
+                if get_pref("remember_window_geometry", True):
+                    set_pref("last_window_geometry", self.root.geometry())
+                    save_preferences()
             # Clean up auto-save and create final backup
             if hasattr(self, "auto_save_manager"):
                 self.auto_save_manager.cleanup()
@@ -686,7 +1096,19 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
 
     def _on_filter_update(self) -> None:
         """Handle filter updates from the search widget."""
-        self.refresh_data_display(apply_filters=True)
+        # Debounce rapid filter changes to avoid repeated heavy refresh.
+        if not hasattr(self, "_filter_debounce_id"):
+            self._filter_debounce_id = None  # type: ignore[attr-defined]
+
+        if self._filter_debounce_id is not None:  # type: ignore[attr-defined]
+            import contextlib
+
+            with contextlib.suppress(Exception):
+                self.root.after_cancel(self._filter_debounce_id)  # type: ignore[attr-defined]
+        # Schedule refresh after short delay
+        self._filter_debounce_id = self.root.after(  # type: ignore[attr-defined]
+            250, lambda: self.refresh_data_display(apply_filters=True)
+        )
 
     def _mark_data_modified(self) -> None:
         """Mark that data has been modified for auto-save."""
@@ -807,6 +1229,13 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
             )
             self._clear_entries()
             self.refresh_data_display()
+            added_date = entry[0]
+
+            def _undo_add() -> None:
+                self.data_manager.delete_entry(str(added_date))
+                self.refresh_data_display()
+
+            self.undo_manager.push(UndoAction(f"Add {added_date}", _undo_add))
         else:
             # Check if it's a duplicate date by trying to load existing data
             df = self.data_manager.load_data()
@@ -822,6 +1251,16 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
                 self.ui_manager.update_status("Failed to add entry", "error")
                 messagebox.showerror("Error", "Failed to add entry", parent=self.root)
 
+    def _undo_last(self) -> None:
+        """Undo the last data modifying action."""
+        result = self.undo_manager.undo()
+        if result:
+            self._mark_data_modified()
+            self.refresh_data_display()
+            self.ui_manager.update_status(f"Undid: {result}", "info")
+        else:
+            self.ui_manager.update_status("Nothing to undo", "warning")
+
     def _delete_entry(self, edit_win: tk.Toplevel, item_id: str) -> None:
         """Delete the selected entry from the CSV file."""
         logger.debug(f"Delete requested for item_id={item_id}")
@@ -833,7 +1272,7 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
             # Get the date of the entry to delete
             date: str = self.tree.item(item_id, "values")[0]
             logger.debug(f"Deleting entry with date={date}")
-
+            deleted_row = self.data_manager.get_row(date)
             self.ui_manager.update_status("Deleting entry...", "info")
             if self.data_manager.delete_entry(date):
                 self._mark_data_modified()  # Mark for auto-save
@@ -843,6 +1282,25 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
                     "Success", "Entry deleted successfully!", parent=self.root
                 )
                 self.refresh_data_display()
+                if deleted_row:
+
+                    def _undo_del2() -> None:
+                        import csv as _csv
+
+                        existing = self.data_manager.load_data()
+                        if (
+                            not existing.empty
+                            and "date" in existing.columns
+                            and date in existing["date"].values
+                        ):
+                            return
+                        with open(self.filename, "a", newline="") as _f:
+                            _csv.writer(_f).writerow(deleted_row)
+                        if hasattr(self.data_manager, "_invalidate_cache"):
+                            self.data_manager._invalidate_cache()
+                        self.refresh_data_display()
+
+                    self.undo_manager.push(UndoAction(f"Delete {date}", _undo_del2))
             else:
                 self.ui_manager.update_status("Failed to delete entry", "error")
                 messagebox.showerror("Error", "Failed to delete entry", parent=edit_win)
@@ -863,7 +1321,9 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
 
         try:
             # Load data from the CSV file once
-            df: pd.DataFrame = self.data_manager.load_data()
+            # Use cached graph-ready data for plotting & base data for table
+            df_full: pd.DataFrame = self.data_manager.load_data()
+            df: pd.DataFrame = df_full
             original_df = df.copy()  # Keep a copy for graph updates
 
             # Apply filters if requested and filters are active
@@ -877,7 +1337,14 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
             self._update_tree_efficiently(df)
 
             # Update the graph (always use unfiltered data for complete picture)
-            self.graph_manager.update_graph(original_df)
+            # Graph gets preprocessed, use dedicated cached transformation
+            if hasattr(self.data_manager, "get_graph_ready_data"):
+                graph_df = self.data_manager.get_graph_ready_data()
+                self.graph_manager.update_graph(
+                    graph_df.reset_index().rename(columns={"date": "date"})
+                )
+            else:
+                self.graph_manager.update_graph(original_df)
 
             # Update status bar with file info
             total_entries = len(original_df) if apply_filters else len(df)
@@ -929,42 +1396,30 @@ Use Ctrl+S to save entries and Ctrl+Q to quit."""
 
         # Use update_idletasks to batch operations and reduce flickering
         try:
-            # Clear existing data efficiently
-            children = self.tree.get_children()
-            if children:
-                self.tree.delete(*children)
-
-            # Update the treeview with the data
+            # Build display dataframe (strip dose columns) once
             if not df.empty:
-                # Build display columns dynamically
-                # (exclude dose columns for table view)
                 display_columns = ["date"]
-
-                # Add pathology columns
-                for pathology_key in self.pathology_manager.get_pathology_keys():
-                    display_columns.append(pathology_key)
-
-                # Add medicine columns (without dose columns)
-                for medicine_key in self.medicine_manager.get_medicine_keys():
-                    display_columns.append(medicine_key)
-
+                display_columns.extend(self.pathology_manager.get_pathology_keys())
+                display_columns.extend(self.medicine_manager.get_medicine_keys())
                 display_columns.append("note")
-
-                # Filter to only the columns we want to display
                 if all(col in df.columns for col in display_columns):
                     display_df = df[display_columns]
                 else:
-                    # Fallback - just use all columns
                     display_df = df
+            else:
+                display_df = df
 
-                # Batch insert for better performance with alternating row colors
+            # Use diff-based update if available
+            if hasattr(self.ui_manager, "diff_update_tree"):
+                self.ui_manager.diff_update_tree(self.tree, display_df)
+            else:
+                children = self.tree.get_children()
+                if children:
+                    self.tree.delete(*children)
                 for index, row in display_df.iterrows():
-                    # Add alternating row tags for better visibility
                     tag = "evenrow" if index % 2 == 0 else "oddrow"
-                    self.tree.insert(
-                        parent="", index="end", values=list(row), tags=(tag,)
-                    )
-                logger.debug(f"Loaded {len(display_df)} entries into treeview.")
+                    self.tree.insert("", "end", values=list(row), tags=(tag,))
+            logger.debug(f"Loaded {len(display_df)} entries into treeview.")
 
             # Process pending events to update display
             self.root.update_idletasks()