/root is a standard first-tier directory in the root directory (as are /bin, /boot, /dev, /etc, /home, /mnt, /sbin and /usr). The root directory is the top level directory on any Unix-like operating system, i.e., the directory that contains all other directories and their subdirectories.

Note that the OP didn't mention the root level, but is talking about its user home directory (/home/<user>/ or ~/).

All standard system directories in the user home directory are hidden directory that start with a '.'. You can probably toggle hidden files via the right-click context menu if there isn't a menu button present.

The subdirectories that are not showing up are not hidden.

/home/userdirectory

  /Books/
  /Desktop/
  /Documents/
  /Downloads/
  /Dropbox/
  /Music/
  /Pictures/
  /Videos/

Of those: "Books" and "Dropbox" are not showing up. The subdirectories are not hidden. The permissions and ownership are the same as the others. But no matter what I do, they do not show up.

I solved the problem. It was something called "firejail" that was install on my system by default.

I did an

1. apt remove firejail --purge

And that seemed to fix it.

Firejail is a sandbox application, so it looks that custom directories that you created aren't white listed and may have to be added to the list of allowed paths.