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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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I don't like the mess some software makes when it install in my system so I want to move it to a more appropriate place.
My questions are:
1- Where is the most appropriated directory for this? (some hidden folder made with this purpose, I thought linux had something like this as a standard)
2- How I move it without breaking anything?
The appropriate directory's are the XDG Base Directory, check this page on arch wiki to move them correctly. You can also use xdg-ninja and it will scan for these extra directories on your $HOME and tell you what you need to do to move them to their appropriate location or not if these directories are hardcoded or cannot be moved.