Unable to update submodule in github due to exist directory

Question

I am using submodule to control my plugin in MacVim. When I tried to update the submodule using git update submodule It comes out:

fatal: destination path 'bundle/ShowMark' already exists and is not an empty directory.
Clone of 'git://github.com/vim-scripts/ShowMarks.git' into submodule path 'bundle/ShowMark' failed

I tried my own solution: remove the directory and then git update submodule It works but the MacVim cannot run properly. MacVim cannot open any new/old files.

Answer 1

a general solution worked for me

git submodule deinit --force . 
git submodule init 
git submodule update --recursive

Answer 2

It'si possible MacVim has issue opening files in bundle/ShowMark because the actual repo name on GitHub is ShowMark**s**(.git).

It might be better if that submodule was register to be in bundle/ShowMarks.
See "How do I move an existing git submodule within a git repository?" for more on that step.