Unix – What are #file# and file~ and how can I get rid of them

To check if a directory exists in a shell script, you can use the following:

if [ -d "$DIRECTORY" ]; then
  # Control will enter here if $DIRECTORY exists.
fi

Or to check if a directory doesn't exist:

if [ ! -d "$DIRECTORY" ]; then
  # Control will enter here if $DIRECTORY doesn't exist.
fi

However, as Jon Ericson points out, subsequent commands may not work as intended if you do not take into account that a symbolic link to a directory will also pass this check. E.g. running this:

ln -s "$ACTUAL_DIR" "$SYMLINK"
if [ -d "$SYMLINK" ]; then 
  rmdir "$SYMLINK" 
fi

Will produce the error message:

rmdir: failed to remove `symlink': Not a directory

So symbolic links may have to be treated differently, if subsequent commands expect directories:

if [ -d "$LINK_OR_DIR" ]; then 
  if [ -L "$LINK_OR_DIR" ]; then
    # It is a symlink!
    # Symbolic link specific commands go here.
    rm "$LINK_OR_DIR"
  else
    # It's a directory!
    # Directory command goes here.
    rmdir "$LINK_OR_DIR"
  fi
fi

Take particular note of the double-quotes used to wrap the variables. The reason for this is explained by 8jean in another answer.

If the variables contain spaces or other unusual characters it will probably cause the script to fail.

Underneath the file system, files are represented by inodes. (Or is it multiple inodes? Not sure.)

A file in the file system is basically a link to an inode.
A hard link, then, just creates another file with a link to the same underlying inode.

When you delete a file, it removes one link to the underlying inode. The inode is only deleted (or deletable/over-writable) when all links to the inode have been deleted.

A symbolic link is a link to another name in the file system.

Once a hard link has been made the link is to the inode. Deleting, renaming, or moving the original file will not affect the hard link as it links to the underlying inode. Any changes to the data on the inode is reflected in all files that refer to that inode.

Note: Hard links are only valid within the same File System. Symbolic links can span file systems as they are simply the name of another file.