OS X spawns from two different cultures: Unix/POSIX and Mac OS.
Folders like /usr, /var, /etc, the command line shell in the Terminal (bash by default) all belong to POSIX environment. Portable software targeting Unix-based systems (like git) go into /usr/local by default, or into package manager's defined location if installed by it (Homebrew uses /usr/local, MacPorts use /opt/local).
Library, Applications, /System and others belong to Mac OS specifically. Apple's software, services, and GUIs of third-party apps go there.
The ~ symbol in path is a traditional way to denote path to current user's home folder. Things that must not be seen by other user accounts go into ~/... counterpart. For example, Mail keeps emails in ~/Library, but standard stationery templates in /Library.
Library folders are supposed to be accessed by applications programmatically, not browsed by user via Finder. Since 10.9, ~/Library is hidden so that users won't unknowingly screw anything there.
There are no out-of-the-box recommendations how to store your files. They will be as good organized as you are good in organizing. They only thing to say in context of OS X is that your files must be in the home folder, but not in ~/Library, and probably not in ~/Public which exists to share files with others.
Best Answer
Depending on who is calculating directory sizes, hard-linked files can easily get counted twice, even though they are really only a single inode and should be counted only once.
The
duterminal command is the surest way to find out how much space a directory is really taking. It never counts hard-linked files more than once.(Caveat. If a file in directory A is hard-linked to a file in directory B, and neither directory is contained in the other,
du Aanddu Bwill each count the file once, so you cannot just add the reported sizes together and get a meaningful sum. However,du C, where C is a directory that contains both A and B, will count the file only once, arbitrarily deciding whether to count the storage as part of A or as part of B.)