Filestructure is something to get used to, but once you get the hang of it, it'll turn out to be quite intuitive.
As for commands: see also the man-pages.
These, you commonly access by typing on the commandline:
man 'some-command'
for example:
man ls
You exit these screens with 'q'.
Depending on the command, these are usually quite comprehensive descriptions of the function, capabilities and sometimes examples.
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