small_stuff

[PaulJonasJost]

Edited some documentation with a PyCharm AI and did my ruff checks. Also removed unnecessary code.

[Copilot]

Pull Request Overview

This PR makes several improvements including documentation updates, removal of redundant code, and various code style enhancements.

• Updated and reformatted settings, logging, and command modules.
• Minor refactoring in the find/replace, context menu, and controller routines.
• Adjusted configuration constants and project setup files.

Reviewed Changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 1 comment.

File	Description
src/petab_gui/views/find_replace_bar.py	Updated UI interactions and search logic; note a potential issue with logical operators.
src/petab_gui/views/context_menu_mananger.py	Added context menu functionality; the file name appears to be misspelled.
src/petab_gui/settings_manager.py	Reformatting and improved coding style.
...	Other files: primarily style and formatting improvements supporting documentation and code cleanup.

Comments suppressed due to low confidence (1)

src/petab_gui/views/context_menu_mananger.py:4

• The filename 'context_menu_mananger.py' appears to be misspelled; consider renaming it to 'context_menu_manager.py' for consistency and clarity.

class ContextMenuManager: