Add this to your .bashrc to get a handy bak function for backing up files and directories

.bashrc

# Create backup copies of files or directories

bak() {
  local name="$1.bak"
  if [ -e "$name" ]; then
    local -i num=2
    while [ -e "$name$num" ]; do
      num+=1
    done
    cp -rv "$1" "$name$num"
  else
    cp -rv "$1" "$name"
  fi
}

As always, don't forget to re-login or source .bashrc after adding.

Usage example:

$ mkdir thesis
$ echo "ABSTRACT" > thesis/abstract.txt
$ bak thesis
'thesis' -> 'thesis.bak'
'thesis/abstract.txt' -> 'thesis.bak/abstract.txt'
$ echo "CONCRETE" > thesis/abstract.txt
$ bak thesis
'thesis' -> 'thesis.bak2'
'thesis/abstract.txt' -> 'thesis.bak2/abstract.txt'
$ echo "INSTANCE" > thesis/abstract.txt
$ tail -vn+1 thesis*/*
==> thesis/abstract.txt <==
INSTANCE

==> thesis.bak2/abstract.txt <==
CONCRETE

==> thesis.bak/abstract.txt <==
ABSTRACT