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Representing a file with a filename, helps users better relate to it. A file though, is really indicated by an inode number. The same goes for each directory, which is just a special file storing the inode numbers to itself (.), its parent (..), the files it contains, and its subdirectories.
To view the inode numbers of a directory, enter:
ls -i (or ls -ai to include hidden files)
To better understand inodes, enter the following two commands:
$ ls -id /usr
293761 /usr
$ ls -id /usr/bin/..
293761 /usr/bin/..
Notice how the .. directory and the usr directory share the same inode.
When you enter ls -l the second column displays the number of hard links. This being the number of files that point to the same inode.
A file will usually have just one hard link, whilst a directory has at least two (e.g. /bin and /bin/.). A directory with four hard links indicates it has two subdirectories, for example:
$ ls -ld /boot
drwxr-xr-x 4 root root 1024 Feb 4 14:48 /boot
4 is displayed because the following directories all point to the same inode:
/boot /boot/. /boot/grub/.. /boot/lost+found/..
Renaming a file or directory doesn't change its inode, and neither does moving it, so long as the file or directory is being moved to the same partition. Copying a file though would give the new file a new inode. (The same going for a directory and its content.)
None of this section you need to know at beginner level, but it does help better understand how things work.
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