How to manage plugins for Vim?

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.