LibreOffice is available from
FlatHub.org. So, I can install it with
sideload. But I can also install it via the
flatpak search, strangely enough, doesn't find it).
Which of these options should I prefer in general?
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After you install a Flatpak app via sideload then all apps from the Flatpak repo you downloaded it from (flathub.org) will show up in AppCenter so you shouldn't need to use sideload for subsequent apps from the same repo.
Personally I prefer installing Flatpak apps on elementary OS if you have the room on your HDD/SSD. The advantages are:
My primary goal was to install as many of my apps as possible using the AppCenter and since eOS 5.1 has support for Flatpak apps I am accepting them as the preferred way to install apps that are not included in the default repositories.
A large part of the Linux community seems to be moving toward Flatpak, Snap, or AppImage. Whether or not it ever replaces traditional package management has yet to be seen. It could be just a fad.
That's the way I see it!
What you 'should' or 'shouldn't' prefer really depends on your environment and your use case. However there is a set of questions which might help you to choose:
Do you want/need the newest version of an app and make sure it is always up to date vs. a well tested allbeit older version? If so Flatpaks and snaps are legit choices, but its important to keep in mind that they are not tested with Elementary OS and if you run a Snap or a Flatpak app you're trusting it to run because your system has Flatpak support, rather then that App being specifically developed and tested for eOS.
Do you custom theme your system? If you, like me are one to install custom themes and stuff like that on your system you might not want to use Flatpaks as they can only adapt to very few themes right now. Maybe in the future this will be a viable option, but as of today there's just not enough support for Flatpaks and custom themed systems to guarantee that it will not break the design principles around which you built your desktop.
How critical is system safety on your system? System safety is important to everybody that much is clear, but is it absolutely critical that no application has access to all parts of your file system and if not, which applications do you want to grant access to the latter? I for example, prefer my browsers and other internet related apps in a containerized format like snap or flatpak, but I will happily use debs and App Center Apps for the rest. Ultimately the question boils down to how cautious you are or have to be. I have no problems to install PPAs from devs I trust either, which however is something that I would never recommend over Flatpaks or AppCenter Apps if the second question is irrelevant to you.
So: Do you want the newest apps, relative system safety and you don't theme your system? Go for Flatpaks or Snaps. I'd recommend Flatpaks since they are now natively supported.
Do you want well tested apps that work and support for system themes and are tested with eOS? AppCenter is the place to be.
Do you think you can trust a developer enough to give an apllication full Disk Access, theme your system and want the newest version? PPAs are the way to go.