The Vim plugin directory under ~/.vim seems messy—a plugin has different files in different directories and the files from different plugins are put together. This is hard to add/remove plugins.
Is there any better method for managing them?
I use pathogen and am very happy with it.
After installing pathogen, any plugins you want to install can be extracted to a subdirectory under ~/.vim/bundle. These plugins will be added to the runtimepath. By this way, each plugin stays in one subdirectory and you can easily add/remove plugins.
Installation of pathogen
Installation on Linux.
mkdir -p ~/.vim/autoload ~/.vim/bundle;
curl -Sso ~/.vim/autoload/pathogen.vim
https://raw.github.com/tpope/vim-pathogen/master/autoload/pathogen.vim
Then, add this to your vimrc:
execute pathogen#infect()
To regenerate help tags:
:Helptags
For more details, please refer to pathogen’s README.