Separate settings and gui state in Settings.json

**Is your feature request related to a problem? Please describe.**

Currently, `Settings.json` mixes Flow-Launcher settings and GUI-related states (e.g., `WindowLeft,` `WindowTop,` `ActivateTimes`). It is hard to manage `Settings.json` using [chezmoi](https://www.chezmoi.io/) or other dotfile managers since those values could change frequently.

**Describe the solution you'd like**

I would suggest Flow-Lancher separate settings and GUI-related states into two files so that `Settings.json` only includes configs directly related to real settings.

**Additional context**

In [How to ignore values frequently changed in a file managed by chezmoi?](https://github.com/twpayne/chezmoi/discussions/3493), the same issue related to managing Scoop config is discussed.

Start by locating how Settings.json is loaded and saved, then trace where WindowLeft, WindowTop, and ActivateTimes are persisted. Separate those GUI-related states from the regular settings and verify that both files are read and written correctly across application restarts.

Written by the indexing model from the issue text.