Only thing i saw here are general answers. /run/user/1000 resp. $XDG_RUNTIME_DIR is a tmpfs (somt. like a ramdisk) created by PAM (pluggable authentication module) on login, 1000 being your user id. It is more restricted in security and size than cache and should be used for small files where quick access or security matters. A common example are sockets.

You can delete it, it will just be regenerated next log in, but your very session will run into trouble, you should log out after (if you don’t just get booted out, that is).

And yeah, like others said; this is not Windows, you don’t have to, and shouldn’t, clean up anything outside your home dir.

https://serverfault.com/questions/24523/meaning-of-directories-on-unix-and-unix-like-systems

• /bin - Binaries.
• /boot - Files required for booting.
• /dev - Device files.
• /etc - Et cetera. The name is inherited from the earliest Unixes, which is when it became the spot to put config-files.
• /home - Where home directories are kept.
• /lib - Where code libraries are kept.
• /media - A more modern directory, but where removable media gets mounted.
• /mnt - Where temporary file-systems are mounted.
• /opt - Where optional add-on software is installed. This is discrete from /usr/local/ for reasons I’ll get to later.
• /run - Where runtime variable data is kept.
• /sbin - Where super-binaries are stored. These usually only work with root.
• /srv - Stands for “serve”. This directory is intended for static files that are served out. /srv/http would be for static websites, /srv/ftp for an FTP server.
• /tmp - Where temporary files may be stored.
• /usr - Another directory inherited from the Unixes of old, it stands for “UNIX System Resources”. It does not stand for “user” (see the Debian Wiki). This directory should be sharable between hosts, and can be NFS mounted to multiple hosts safely. It can be mounted read-only safely.
• /var - Another directory inherited from the Unixes of old, it stands for “variable”. This is where system data that varies may be stored. Such things as spool and cache directories may be located here. If a program needs to write to the local file-system and isn’t serving that data to someone directly, it’ll go here.

Something to realise when starting with Linux is that everything is a ‘file’. Sockets, processes, input, output etc. That’s very different from Windows and part of why scripting on Linux is so powerful. You can interact with anything.
So some directories are filled with things that aren’t necessarily files but look like it. Someone else posted a whole list, just realise that under those directories/paths shouldn’t be messed with unless you know what it’s for.
Generally when you’re getting used to Linux, /home/$user (aka ~) is where you put personal things. The rest is managed by OS and applications, don’t worry about it.
Edit: spelling

/run contains all sorts of virtual stuff, it doesn’t persist over a reboot,

I would advise against deleting anything in it as those files are used by programs running as whether user has the ID of 1000 (most likely you)

it contains things such as sockets and lock files so that programs can interact with each other

I’d say a good rule of thumb for a beginner is not to touch anything outside of their own home directory. Modifying or deleting files in other locations is an easy way to break your system.

Don’t delete it. It’s an area of the filesystem where the current user session data is kept. This includes things like sockets to communicate with other session components and lock files. It’s usually hosted on a ram disk so takes up no space in the system and goes away when you shutdown your machine.

Then I got a lot of duplicate files. For example in subfolders relating to my mp3 player I even discovered my whole NextCloud ‘drive’ is there again: /run/user/1000/doc/by-app/org.strawberrymusicplayer.strawberry/51b78f5c/N

In Linux a file can show up several times in the filesystem without being duplicated. Symbolic links and hard links will cause this to happen, and they’re a normal part of organizing the filesystem. Just because you see a file in several places, that doesn’t mean disk space is wasted with duplicates. There may be only one physical copy of the file, appearing in multiple places. With hard links you need to be especially careful about deleting, since you’ll think you’re deleting one of several duplicates but you’ll in fact delete the only copy of the file.

Never touch anything in /run directory.

Other people already answered the question, I just want to say that this question was incredibly well asked.

The most important thing to realize about the “file system” in Linux is it does a lot more than just persist your documents and app data. You shouldn’t index your root directory because almost everything other than your home directory is some kind of Linux distro/application-specific directory that is often not a normal directory stored on a storage device. If you run the mount command with no arguments, every line of output is a separate file system, mounted at some specific directory of the current “mount namespace”. Kinda confusing, but every process in Linux has a mount namespace that has a list of mounted file systems, often that namespace is shared between many/most processes, such as your terminal shell. Most of the file systems will be virtual i.e. not representing anything in storage. For example sysfs (always mounted at /sys), proc (always mounted at /proc), devtmpfs (mounted at /dev), etc. are all completely virtual and are ways for system services and applications to access state and devices exposed by the Linux kernel. They should never be indexed, treated as normal files, or modified by the user.

That’s probably even more confusing, sorry. But the gist of it is, the only directory on your system you can really count on actually being stored on disk and always available to you is your home directory. Basically everything else exists as an implementation detail of the operating system and software applications.

If I were you, I’d stick to only indexing your user home directory. Indexing /usr or /tmp or /etc or whatever is like indexing C:\Windows and C:\Program Files, except even weirder since at least on Windows those are actually files stored on disk whereas in Linux they may not even be actual files (although most of them in /usr and /etc are actual files on disk).