Background-Story: I did a "flatpak update" on a remote client and every package wants the PW for downloading and for installing again. I had to enter the password like 30 times or more.
this post was submitted on 06 Mar 2024
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Any package manager worth its CPU cycles should take care of orphaned dependencies for you. Whether your package manager is decent or not is matter of heated debate, but the problem of orphaned dependencies has been largely solved.
TLDR, you're likely wrong about it. You're also paying to have a neat filesystem by using more storage (which is cheap, spend away), memory (a bit or a big bit, depending), and performance (there are comparisons online, only you can decide if it's significant for you).
Now, my opinion is that you're overtaxing yourself. The reason you mentioned for adopting flatpack is better addressed by familiarizing yourself with your main package manager. People that defend widespread use of flatpacks usually have other reasons (mostly newer versions, faster bug fixes and security fixes, etc.).
The combination of which distribution and how to use side-loaded software isn't a one size fits all. There are pros and cons to each approach, and they differ based on your needs, your distro, your threats...
Thanks for answering! I'll do some reading on how package managers work.
Good luck. That's like "reading on how software works".