[WIP] Refactor Emacs configuration to follow 2024 best practices

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Original prompt

Act as an Emacs Lisp expert specializing in modern Emacs (version 29+). Refactor the attached configuration to follow 2024+ best practices:
Native use-package: Replace any manual require or install logic with the built-in use-package macro. Use :vc for packages that need to be fetched from source.
Built-in Alternatives: Identify third-party packages that can be replaced by built-in libraries (e.g., replace projectile with project.el, ivy/helm with vertico/marginalia, or flycheck with flymake) unless I have specific custom logic for them.
Byte-Compilation & Startup: Ensure all use-package blocks use :defer t or appropriate autoloads to keep startup fast. Move GUI-specific settings (tool-bars, menu-bars) to early-init.el logic.
Modern UI: Enable pixel-scroll-precision-mode and ensure display-line-numbers-mode is used instead of the older linum-mode.
Clean Syntax: Use setopt instead of setq for user-customizable variables where appropriate (available in Emacs 29+).

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