Run ruff format changes and finalize indentation and lint fixes.

MIGRATION.md

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+# Migration Guide: Canonical Imports and Running TheChart
+
+This project now uses the canonical package `thechart.*` for all imports.
+
+What changed
+- Legacy shim modules under `src/` (e.g., `src/ui_manager.py`) remain only for compatibility and now emit `DeprecationWarning`.
+- Canonical modules live under `src/thechart/` and should be imported directly.
+
+Do this
+- Imports:
+  - from thechart.ui import UIManager, ThemeManager
+  - from thechart.analytics import GraphManager
+  - from thechart.data import DataManager
+  - from thechart.export import ExportManager
+  - from thechart.managers import MedicineManager, PathologyManager
+  - from thechart.search.search_filter import DataFilter, QuickFilters, SearchHistory
+  - from thechart.core.logger import init_logger
+  - from thechart.core.constants import LOG_LEVEL, LOG_PATH, LOG_CLEAR, BACKUP_PATH
+  - from thechart.core.auto_save import AutoSaveManager, BackupManager
+  - from thechart.core.error_handler import ErrorHandler, OperationTimer, handle_exceptions
+  - from thechart.core.preferences import get_pref, set_pref, load_preferences, save_preferences, reset_preferences
+  - from thechart.core.undo_manager import UndoManager, UndoAction
+  - from thechart.validation import InputValidator
+
+- Run the app:
+  - python -m thechart
+
+Avoid this
+- from src.ui_manager import UIManager (deprecated)
+- from ui_manager import UIManager (deprecated)
+
+Notes
+- Deprecation shims will be removed once all usages are migrated.
+- Tests will be updated separately to import from `thechart.*` directly.