Consider each distro like a house of kung-fu.

We are all hitting dummies, we are all practicing falls, drops, and stances, but we have different names, cultures, methods and ideas of getting those same goals done.

So what’s the benefit of having programs each installed in separate locations that are wildly different?

Installing an Appimage or flatpak almost entirely leaves that program inside your Home folder, meaning, if you were to reinstall your base system, even a different distro… within reason, those apps would still continue to function, all of their libraries and connections made within a folder that didn’t change.

Linux is about aversion to risk. On Windows, you’d backup and restore your entire system. Linux brings into question what you consider “your system”. Some distributions can be entirely rebuilt from the ground up via a text file’s instructions and nothing else.

My main desktop can be back up and running from a complete SSD failure in 20 minutes, a combination of backups and a saved Archlinux installation config for that system.

You should try NixOS or something similar. It sounds like all of your gripes with Linux are solved by NixOS. It makes system management a LOT more sane than FHS has gotten.

Why not consolidate all this?

https://xkcd.com/927/

But, there is actually a location standard: https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard

What you’re seeing is the result of decades of new ways to install stuff being added at different times. As a new way is added all the old ways still need to work because getting everyone to switch to the new way is impossible. There is no central authority making these decisions, it’s more of a marketplace of ideas with different ‘sellers’ competing for attention.

Linux doesn’t really have stand alone programs like Windows. A package is a series of files that get placed in the proper places plus some optional scripting. Packages have dependencies so you can’t just run a binary from a package. The closest thing Linux as is AppImage but it lost a lot of steam.

In Linux there are two general types of package managers. The first one is native packages. Native packages install to the root filesystem and are part if the core system.

The second type of package manager is the portable format like Flatpak. Flatpaks can either be installed system wide or as a local user. The big difference is that they run in there own environment and have limited permissions. This is done by creating a sandbox that has its own filesystem so that it is independent of the system. This is also what makes them portable as that environment is the same no matter what.

Technically snap packages are portable but you aren’t going to see much use outside of Ubuntu since the underlying architecture has so many flaws.

This is part of why these days I just stick to flatpaks. No fragmentation, same on any distro, I know where all the programs are going as well as all their config files.

If I want to back up my flatpaks I can do so trivially.

It’s a godsend. Way better than having a bunch of different formats everywhere, or the windows-style some programs installed in XYZ directory, some in program files, some in program files (x86), with config files saved literally anywhere. Maybe it’s in one of the dozens of poorly laid out appdata folders, maybe it’s where the exe is, maybe it’s in documents, maybe it’s in C:, maybe it’s hidden in my user directory, etc. I’ve even seen config files saved to bloody onedrive by default, leading to some funky app behaviour when I wasn’t connected to the internet, or when I ran out of onedrive space.

Linux is actually kinda designed to be less fragmented than windows really.

The reason you don’t pick an install directory is because the standard is that binaries live where binaries live, dependencies live where dependencies live, logs live where logs live, etc.

All the user should worry about is where the media or whatever your program works with is.

Always try to find the apt install instructions for whatever program you want, and it’s easy to uninstall with apt remove.

Apart from a few deb packages, almost everything that can’t be managed via apt should be considered incomplete or experimental. If it was ready for you to just use it without issue, it would be in an apt repository.

It may seem a bit daunting to have to use command line at first, but once you’re used to it, you’ll realise how absolutely broken and archaic managing software on windows is. (Like seriously, it’s 2024 and you’re still having to fish through slow or sketchy websites to find installers for tools and drivers.)

Windows certainly doesnt have uniformity.

Where are my game saves located?

Are they in my hidden AppData folder? If so, which of the three subdirectories does it live?

If not there, then surly it’s in the Saved Games folder.

Nope. It must be in My Documents.

Shit… Maybe in the Program Files?

For fuck sake, where is it?!

Web browser > search > pcgamingwiki (great resource BTW), save game location. AH-HA! IT’S IN… My Documents?

I just checked there! (Half an hour passes)

Found it! Now why the FUCK does Windows partition the local user directory from the OneDrive user directory?!

Windows is a FUCKING mess. Once you get used to Linux, you’ll understand the worst thing is Mozilla thinks it’s okay to put its config file one directory up from where it should be.

The idea is to not manage programs by hand to avoid messes.

The multiple solutions come from various needs, but it’s more of an underlying complexity of installation than a real intent to have so many.

Ideally we would need one clean package manager that handles everything without ever having to tinker with installation paths and various methods.

I don’t see the issue, since you rarely have to run a program by going to the location of the binary (AppImage and others excluded).

First of all, in Linux everyone should only use software from distribution repositories (eg. via apt command in Debian, Ubuntu, Mint, dnf/yum command in Fedora etc…). Package managers will install software in controlled way and it is really easy to remove them too. And, there is usually gui app for installing apps from distribution repositories.

Second way is to use flatpak / snap. They are pretty much similar and will keep things easy.

Do not install sh packages or tar.gz if you really do not know what you are doing. These are only for expert cases.

One fundamental change coming from Windows is that in Linux, you should never worry about location where software is installed (except for those expert cases, which you should not use). They will be put in correct places always. In Linux, apps are sorted so that executables go to /usr/bin, library files to /usr/lib64 and /usr/lib, applicatoin other non-modifiable stuff to /usr/share etc. It gets quite a lot to get used to, but in long term it feels more natural than Windows way to dump everything in app directory.

My recommendation will be to install some user friendly distribution (Ubuntu, Fedora, Mint) and just go ahead with default package management things what it offers. If you see Android way handling software good, Fedora Silverblue is kind of like that - System upgrades are handled same way, and applications are installed as flatpaks.

You can install programs with sudo apt get (program). You can get programs with snaps. You can get programs with flatpaks. You can install with tar.gz files. You can install with .deb files. You can get programs with .sh files.

APT, the Advanced Packaging Tool, uses .deb files. Speaking technically, APT is the app store part of the system, the part that actually installs packages is called dpkg. If you have a .deb file and you want to install it, you can directly invoke dpkg. I have encountered things like printer drivers where the vendor will provide in .deb format. For one reason or another they’re doing it the way the Debian/Ubuntu standard package manager does it, but not publishing the files to the repositories.

Snaps, flatpaks and appimages are intended to solve the problem of fragmentation. See, APT with it’s .deb files are the Debian system used by most if not all Debian/Ubuntu forks. DNF with .rpm files are Red Hat/Fedora’s system. Arch uses Pacman with .pkg.tar files. SuSe, Nix, and a couple others have their own systems, and none of them interoperate.

One thing these do have in common is where they put the files they install; they are sorted by type and function into several directories in the root directory. Most of them you’ll find in the /usr directory, such as /usr/bin, /usr/sbin, /usr/lib or /usr/share. bin for binary files, this is where executables like sh or bash or cat or grep. sbin is for binary files that are only for those with super user privileges; you have to switch users to root or use something like sudo to execute those. Non-executable files like libraries, data, assets etc. will be variously stored in lib, local, share and so forth. You may find there are duplicate folders, like /bin and /usr/bin. In the olden days of minicomputers these were often located on separate drives, but nowadays /bin is a symlink (basically a shortcut) of /usr/bin. Some of that is maintained for backward compatibility or in case you still need to use the differences. It gets a lot more nuanced than I’m talking about here.

They aren’t installed in /home/$USER because if you have multiple users on the machine you probably want them all to have access to the software. Say you’ve got a husband, wife and two kids, would you want to have to install four copies of LibreOffice?

If you do want to install software in the user’s home directory, the place to do that is probably /home/$USER/.local/bin

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This does indeed make it a pain in the ass to publish software for Linux. So they wanted one system that would work on most if not all distros. Of course three competitors arrived.

Snap is Canonical/Ubuntu’s attempt which IIRC started with their embedded systems but they’ve been pushing as their whole deal. It’s the closest thing to an Apple App Store there is; it’s owned by Canonical, the back end is proprietary so no one else can host the Snap repository, etc. A lot of folks don’t like that they kept some of it proprietary, plus there are performance issues with how it’s implemented; it mounts virtual disks for each app installed from Snap (or something similar to that) so it gets messy.

Flatpak I think sprung up in or around the Fedora side of the world but has always had the goal of being omnicompatible. It is totally open, you can host your own flatpak repo if you want, though the de facto standard repository is Flathub. At this point, I think Flathub has achieved the goal of being the one place where, if you have a commercial app you want to also publish a Linux version of, publishing it as a Flatpak will reach most of the Linux audience in one shot. There are a couple downsides to it; for example Flatpak isn’t a great way to distribute command line tools, but for GUI-based applications it works fine. Flatpaks are weird; they tend to install in /var somewhere, I think for reasons surrounding permissions.

Appimage is also around; the technique here is it’s basically a .iso file that has everything the app will need to run in it, so you mount the .iso and run the executable file inside. No infrastructure or installer needed. There are package managers for it, but they aren’t required. I find appimage to be the one to use if you’re making some small niche software that 200 people in the world will ever want and you don’t want to bother with the repositories, but I don’t like using them for main distribution.

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Let’s change gears and talk about .tar.gz or .run or .sh files. These are non-standard ways of installing software on Linux and I would avoid them unless it’s a last resort type of situation.

A .tar.gz file is functionally similar to a .zip file on Windows; it’s a TAR file (Tape ARchive. A bunch of files packaged into one continuous file, initially designed to be written to magnetic tape) which has been compressed with GZip. When software is distributed this way, it is up to the user to extract and store it…somewhere. Probably the best place to do this is in /opt, which is the standard location for pre-compiled software manually added to the machine by the administrator.

.run files have basically no standard and can do damn near anything and are a bad idea. It could be written in any language and do anything. You just don’t know. The one I encountered the most was Simplify3D’s installer; what they did was directly translate their Windows installer to Linux, the way Windows install wizards work, rather than do things in a Linux way. Hopefully you don’t have to deal with that.

a .sh file is a shell script. Once again these can do anything but it’ll be a text file full of shell commands that you can read and understand. It’ll probably consist of a series of commands like wget or curl which download files from the internet and then commands to put them where they need to go in the file system. Once again this tends to be the approach for the “I’m usually a Windows guy but here’s my Linux version” folks. This is going to choose where to put software for you, hopefully in /usr/local.

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You may also find yourself compiling software from source code, which is what’s happening when you’re told to go to Github and then run a series of instructions like git clone, make, make install. Make is basically a scripting system specifically for compiling software, it will figure out what to do. I believe locally compiled software ends up in /usr/local/bin.

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Summary: There are a lot of directories where software ends up, and it’s done the way it is so you can tell by where it is stored what it is, what it does, who has access to it, who manages it and how it arrived on the system. It also keeps automatic processes like the package manager from interfering with software manually installed or compiled by the users or system administrators.

I understand fragmentation here, as you can get what you need in a format that works well-enough.

Different package formats often have technical differences. Recently I had the choice to use something from a flatpak to reduce lib32 dependencies on my system… but I didn’t go with that as the other dependencies it needed (openGL, graphics driver etc) were redundant thanks to sandboxing (~2GB download!).

Anything native from itch, GOG, or humble doesn’t really ‘install’ but rather they are just extracted… so the files should be what it is (portable, except game saves/user data likely won’t be). This allows you to run it off of a slower+larger-capacity drive.

EDIT: Also if you need to compile it, probably will also just compiled to where you put it (to a bin folder).

Non-system stuff like this is more viable for things that you don’t need updated frequently/ever (particularly games/software post-development). For sure most-of-the-time the best experience is via your package manager.

If you delete a program from the Programs folder, does it get uninstalled from the system? Nope. You have to go drag the registry and delete any mentions. You have to go looking for shortcuts and delete all those in multiple locations. If you go to the control panel -> add/remove programs, that works decently, but it’s not guaranteed. It’s been a couple decades since I’ve used windows regularly, but there were all kinds of folders, appdata roaming and that’s just what I remember having to go dig through because there is no real standard for anything. That doesn’t even get into system files and dlls.

There are package managers for Windows too. Choclatey is something I have seen in README.md files for various install instructions.

The Unix-like install locations are for organization. Goes back to Unix-like server oses. Linux is Unix-like as well. Linux doesn’t have a registry to keep track of all the locations for all the files and configurations for each program, so organized locations where the system can expect to find specific things is how it’s done. I much prefer the organized file structure, digging through the registry where there is only the minimal organization was something I always hated.

I think that, while, yes, fragmentation hinders a system, it is also its saving grace, as it also stops a given family of systems from growing into what made the competition problematic.

Taking the Program Files folders as example, they have limited read/write permissions on Windows, so whenever possible, I try to install them onto a folder I make in the root of C:. But more and more, since at the very least Windows XP from what I could observe, Microsoft is training users into using only the users folder, and less and less programs give an option to install elsewhere, installing only on the Program Files folder instead. Meanwhile, on Linux Mint (my distro of choice), if AppImage (my to go medium of programs) isn’t working well, I can always fallback to other means, such APT directly or downloading its .deb files then extracting them, getting from flatpak, compiling it myself, building a custom AppImage, running on a VM or emulator, or in the worst possibility, I make a dual boot between Mint and some other distro.

Also, although there are many package managers, from my experience, they usually work similarly. Some changes in syntax, options and names, but nothing outlandish. It would be, I think, like someone learning a close language to his/her mother tongue. And from experience, you can even organize installations in a more standardized way, although it will take some effort from your part to figure out how, since some adaptations may be needed (java 8 and sdl ptsd intensify).

And lastly, from what I can observe, stuff in Linux more often than not share logic or even methods with a lot other stuff in the system. Dunno if it’s a bit of a bias of someone that’s using Linux for a few years already, but the fragmentation usually feels superficial to me, with distros being more tweaks of the ones they stem from, and major changes being better observable when distros are sufficiently far apart.