Unfortunately, Linux manuals are pretty scattered around. I’ll try to find something for you:

• If you want to learn the very basics of Linux command line, here’s what I found on the web: http://www.ee.surrey.ac.uk/Teaching/Unix/ ;
• For on how to use GNU user-land tools (Bash, cat, less, grep, sed, etc.), I recommend the GNU manuals which are very well-written: https://www.gnu.org/manual/blurbs.html (example: Bash manual);
  • GNU manuals are also downloaded for offline read by default. These manuals are provided with info.
• For GUI desktop, it depends on what Desktop Environment (DE) you use:
  • KDE wiki with tutorials: https://userbase.kde.org/Tutorials
  • GNOME app overview with documentation: https://apps.gnome.org/
  • If you don’t know what DE you use, KDE uses sharp edges for windows and GNOME uses round edges ( 👁️👄👁️ ).
• For system, as @[email protected] pointed out, for system-specific stuff, there’s ArchWiki that has topics about everything.
• If you want to understand what are the /usr, /usr/local, /etc, /dev, etc. filesystem directories, you want to look at the Filesystem Hierarchy Standard: https://refspecs.linuxfoundation.org/FHS_3.0/fhs/index.html
• There is also a free training course for Linux: https://training.linuxfoundation.org/training/introduction-to-linux/
• If you’re a developer and want to find out how deep the rabbit hole is, you may want to look at an online book Operating Systems: Three Easy Pieces: https://pages.cs.wisc.edu/~remzi/OSTEP/

EDIT: Forgot this important material:

• If you need to know command-line argument specifics for a particular program, use manpages (For example, to find brief information about grep, type man grep in your shell, and info grep if you need a complete manual).