This may be a dumb question but I can't seem to figure out why a php file with the same name is created but with extension index.php~ after I finish editing index.php file on my remote server using vim.
I quit the vim editor with :wq! command, on Windows the ~ in file extension usually mean unsaved or file that is currently opened, is it the same thing on Linux server?
index.php~ is backup and contains a file as it was before you edited index.php
You can disable this behavior in your .vimrc file:
set nobackup