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the question of how you reset to a known-working state if it mutates itself

I have this problem on my computers already, because configuration files and other program data is spewn across all kinds of directories and files all over the place.

The only two options I have is a) do a factory reset and reinstall software from scratch and spend time configuring things again, or b) live with all of the extra garbage that has been excreted by the software on my systems just so that I can keep the data that I actually want to keep.

Whereas to pick up all of my data that I do care about and copy only that and nothing extra to another place, is extremely time consuming to the point that it’s not realistically doable :(

Of course, cramming absolutely everything including user documents into the program won’t solve that either.

My ideal system would separate data that was written because of me (non-default config values, bookmarks, etc) from documents etc made by me, from garbage that the program wants to write that I absolutely do not care about and do not want to know about.

Look, I try to avoid bringing up nix in unrelated conversations. But.

The only two options I have is a) do a factory reset and reinstall software from scratch and spend time configuring things again, or b) live with all of the extra garbage that has been excreted by the software on my systems just so that I can keep the data that I actually want to keep.

NixOS solves this.

My ideal system would separate data that was written because of me (non-default config values, bookmarks, etc) from documents etc made by me, from garbage that the program wants to write that I absolutely do not care about and do not want to know about.

And NixOS with https://github.com/nix-community/impermanence does this, forcefully. Actually normal nix might solve it depending on how far you want to go.

Again, I wouldn't usually try to evangelize it, but you have described your ideal system, and it exists.

While way too restrictive, I believe android actually has the correct idea here, having separate data folders per app. The problem is that you can't really touch this per app data folders - even backup is a special operation only doable by the OS (or you root the phone).

Spamming my home folder on the other hand is criminal..

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