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My DoxygenToolkit.vim was installed this way.

1.To open `Root Terminal`  with root password
2.mkdir -p   /usr/share/vim/vim74/bundle
3.git clone https://github.com/gmarik/Vundle.vim.git /usr/share/vim/vim74/bundle
4.vim  /etc/vim/vimrc
set nocompatible              
filetype off                  
set rtp+=/usr/share/vim/vim74/bundle/Vundle.vim
call vundle#begin()
Plugin 'VundleVim/Vundle.vim'
Plugin 'tpope/vim-fugitive'
Plugin 'L9'
Plugin 'git://git.wincent.com/command-t.git'
Plugin 'file:///home/gmarik/path/to/plugin'
Plugin 'rstacruz/sparkup', {'rtp': 'vim/'}
Plugin 'ascenator/L9', {'name': 'newL9'}
call vundle#end()            
filetype plugin indent on    
5.vim  /etc/vim/vimrc
Bundle 'DoxygenToolkit.vim'
6.To open vim 
:BundleInstall

Now DoxygenToolkit.vim was installed.
I find that two problems remain here.
1. To open vim with root user
Some error messages occur.

vim
Error detected while processing /root/.vim/bundle/newL9/plugin/l9.vim:
line   40:
E174: Command already exists: add ! to replace it
line   89:
E174: Command already exists: add ! to replace it
line  100:
E174: Command already exists: add ! to replace it
line  104:
E174: Command already exists: add ! to replace it
Press ENTER or type command to continue

2.To open vim with regular user.

:DoxLic
E492: Not an editor command: DoxLic 

How to fix them all?

2

The problem seems to lie in ascenator/l9 plugin. Open it at the lines incriminated and add a ! on all command definitions. The best is to contact its author to have him fix the plugin.

The fact you're using using the official plugin and a fork of it certainly doesn't help. Why are you doing this? It gives me the impression you have copy-pasted stuff from other people configuration without really knowing why they have these lines in their configuration.

I'm under the impression there is something fishy about the way you use Vundle. As I use VAM, I can't tell if this is correct, I'll let other people using these plugin managers help you with these lines. The fact the configuration is done at root level (/etc) may not simplify things.

PS: In lh-cpp I provide Doxygen snippets and a :DOX command that analyses function signatures (it tries to deduces in and out parameters, (deprecated) throw specifications, trivial preconditions, and so on -- I still have to extract template parameters). But to be perfectly honest your problem seems to be completely unrelated to doxygentoolkit.

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