I would just stick to pathogen until you get familiarized with how things work. I started moving things to the 'pack/yourname/start' one day and things started breaking. That being said I am working on a plugin and 'pack/myname/start' seems to work fine. Pack is a great way to separate your plugins. If you notice tpope plugins usually go in there.
I couldn't deal with the hassle. So I just installed neovim and installed standalone vim. I figured most online articles and documentation will refer to standalone vim too.
Things worked straight away.
This works for my python files.
zM folds the file to the lowest number of lines, then zo unfolds the line that is folded to show functions in classes which can be searched, then when you want to look at a function content, goto its folded lines and unfold all with zO.
You shouldn't alter the base vim configuration. Instead, you should put this in your user's vim configuration directory, which on macOS would be ~/.vim i.e. ~/.vim/autoload/plug.vim.
To answer you actual question as to why it is removed as soon as it is downloaded, how are you trying to write to that directory? As you mention "save file as" I can ...
oh, I have found the solution. This is for others reference.
vim probably can not expand ~/ to $HOME. In my .bashrc, I had
changing that to
solved the problem.