A single app is not necessarily a good thing, I would argue that you’re already using multiple apps on your day-to-day work, and it would be better if remote connectivity were integrated into those. For example, you mentioned a side-by-side view of two locations, this is a normal workflow on day-to-day even without remote access, sometimes you want to have your file explorer split the view in two and look at two folders simultaneously to perform operations, ideally this exact same flow should be able to connect to any remote host and show it to you seamlessly, so you can use the same flow for copying stuff from folder A to folder B regardless of the folders being in different machines.

Unified hierarchy doesn’t make much sense for remote connections. I see why you would want to have some organization as in groups of machines, but I don’t understand what you mean by hierarchy. In any case ssh/config is a unified source of truth for this that all of the commands you mentioned (and many more) use when trying to connect remotely via ssh.

You know the name of the tool, what’s the problem with using the tool directly? For ssh you’re going to be dropped in a terminal, so starting in a terminal should be acceptable, for VNC or RDP whatever client you use should be able to parse the ssh/config files so you’re not duplicating information, for SFTP or SCP you should be using your default file explorer as of the other machine were a different folder, there’s no need to have a separate app for it (also you should consider looking at rsync since it’s much better than naively copying files over).

I know it’s not the same as you’re used to, but it’s one of the core differences in philosophy from Windows to Linux. The philosophy on Unix in general os for an app to do one thing, but do it well, so it’s much more common to use different apps for different stuff than having a monolithic app that does everything but nothing perfectly. That being said, the closest I know of for what you’re asking is Remmina, although I use it only for RDP since for ssh and rsync I prefer a terminal (and since I have the hosts configured I get tab completion as if they were local folders). That being said I only have a handful of machines to connect to, so I don’t need any sort of organization on them, and when I had dozens of machines to attend to I used Ansible and other stuff to perform bulk actions per group and other maintenance stuff.

I hope Remmina works for you, or that you find something that does, unfortunately I think that might be very hard because of the philosophical differences from Linux to Windows, in general Linux users prefer that their default file manager be able to connect via ssh using the default ssh configs than a secondary ssh manager that can browse files but is neither the source of truth for ssh nor the default file manager. I know I keep using the same example, but it is very telling of the difference in philosophies (and yes, most if not all of the file explorers in Linux can in fact connect via ssh using your default configs).

It is obviously not the same as manually making all these connections and using different apps for each of them and backing them up with git.

I mean, that’s the whole unix philosophy. Rather than one big monolithic app, we use dozens of tiny ones that can all be scripted and work together. I think I’d just use an org-mode file to create the sort of centralized UI you’re describing.