I somewhat had the crazy hope there was a way to somehow overlay a filesystem over / for the context of an app, and so that it would really be transparent.

There are a couple of options for that. But wouldn't it be the cleanest solution to solve it right in the source code from the beginning, by not using absolute paths? (How is it done for macOS)?

Effectively, it is exactly what you'd do if you target the macOS or Windows platforms.
Unfortunately those are terribly painful, so it's not really a selling point :)

Well, the user's perspective is the opposite: With Windows, we can get your "original" software, directly from the developers, in the way the developers want it...

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