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Cleaning up the whole $HOME/<.pkgname>/ situation for individual app settings
(iusearchlinux.fyi)
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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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What ended up happening with me was I just have all my stuff in a separate /stuff partition. That way I don't need to worry about dotfiles cluttering up my actual data. I also use NixOS Home-Manager to manage my dotfiles for things like git and vscodium.
I'm a recent transplant from windows to linux and I saw this coming. My Documents is not reserved for documents that are actually mine, I had no expectation /home would be any different, and it seems I was correct. Other than some things I want quick access to (downloads, notes, scripts) I keep everything I care about organized under /data.