PluginClean removes vundle itself

[huahaiy]

Run PluginClean, get below, which remove Vundle itself.

" Removing Plugins: |
Plugin 'bubblegum' |~
Plugin 'vim-eastwood' |~
Plugin 'vim-monokai' |~
Plugin 'Vundle.vim'

[jdevera]

That means you are missing a line in your vimrc that says: Plugin 'gmarik/Vundle.vim'

[huahaiy]

I have that line. Otherwise, I won't be able to use PluginClean, right?

[jdevera]

Not necessarily. Can you please post your vimrc?

[huahaiy]

""""""""""""""""""""vundle""""""""""""""""""""""""""""
set nocompatible " be iMproved
filetype off " required!

if has('win32') || has('win64')
set rtp+=/vimfiles/bundle/Vundle.vim
call vundle#rc('$HOME/vimfiles/bundle/')
else
" Usual quickstart instructions
set rtp+=/.vim/bundle/Vundle.vim
call vundle#begin()
endif

" let Vundle manage Vundle
" required!
Plugin 'gmarik/Vundle'

" My Bundles here:
"
" original repos on github
Plugin 'tpope/vim-sensible'
Plugin 'tpope/vim-fugitive'
Plugin 'tpope/vim-surround'
Plugin 'tpope/vim-classpath'
Plugin 'tpope/vim-projectionist'
Plugin 'tpope/vim-dispatch'
Plugin 'tpope/vim-fireplace'
Plugin 'guns/vim-clojure-static'
Plugin 'guns/vim-clojure-highlight'
Plugin 'ekalinin/Dockerfile.vim'
Plugin 'kien/ctrlp.vim'
Plugin 'luochen1990/rainbow'
Plugin 'davidoc/taskpaper.vim'
Plugin 'othree/xml.vim'
Plugin 'ervandew/supertab'
Plugin 'scrooloose/nerdcommenter'
Plugin 'scrooloose/syntastic'
Plugin 'jcf/vim-latex'
Plugin 'chrisbra/csv.vim'
Plugin 'jnurmine/Zenburn'
Plugin 'junegunn/seoul256.vim'
Plugin 'majutsushi/tagbar'
Plugin 'bling/vim-airline'
Plugin 'Shougo/neocomplcache'
Plugin 'Shougo/neosnippet.vim'
Plugin 'venantius/vim-cljfmt'
" vim-scripts repos
Plugin 'L9'
Plugin 'paredit.vim'
Plugin 'JSON.vim'
Plugin 'matchit.zip'
Plugin 'Vim-R-plugin'
Plugin 'xoria256.vim'
" non github repos
"Bundle 'git://git.wincent.com/command-t.git'
" ...

call vundle#end()
filetype plugin indent on " required!
"
" Brief help
" :PluginList - list configured bundles
" :PluginInstall(!) - install(update) bundles
" :PluginSearch(!) foo - search(or refresh cache first) for foo
" :PluginClean(!) - confirm(or auto-approve) removal of unused bundles
"
" see :h vundle for more details or wiki for FAQ
" NOTE: comments after Bundle command are not allowed..

""""""""""""""""""""General""""""""""""""""""""""""""""
syn on

set tabstop=2
set shiftwidth=2
set expandtab

set autoindent
set smartindent

" folding by syntax
set fdm=syntax

" matching brackets
"set showmatch

" hightlight search
set incsearch
set hlsearch

" show cursor position
set ruler
set cursorline

" show statusline
set statusline=%<%F%h%m%r%h%w%y\ %=\ lin:%l,%L\ col:%c%V\ %P
set laststatus=2

" get ride of the annoying bell (both sound and flash)
set vb t_vb=

let mapleader=","
let maplocalleader=","

" insert current time
nmap ct :execute "normal i" . strftime("%x %X (%Z) ")
imap ct :execute "normal i" . strftime("%x %X (%Z) ")i

" For those with sadly no function keys available, toggle spelling use \s
imap s :setlocal spell! spelllang=en_gb
nmap s :setlocal spell! spelllang=en_gb

" paste mode toggle
nmap p :set invpaste

""""""""""""""""""""Color""""""""""""""""""""""""""""
if has('win32') || has('win64')
set t_Co=16
set term=win32
colors zenburn
else
set t_Co=256
set term=xterm-256color
colors seoul256
"colors xoria256
endif
" keep the terminal's background color (e.g. stays transparent)
hi Normal ctermbg=NONE
hi NonText ctermbg=NONE

""""""""""""""""""""Clojure""""""""""""""""""""""""""""
let vimclojure#WantNailgun = 1
let vimclojure#HighlightBuiltins = 1
let vimclojure#DynamicHighlighting = 1
let vimclojure#ParenRainbow = 1
let vimclojure#SplitSize = 15

""""""""""""""""""""LaTex""""""""""""""""""""""""""""
" IMPORTANT: win32 users will need to have 'shellslash' set so that latex
" can be called correctly.
set shellslash

" IMPORTANT: grep will sometimes skip displaying the file name if you
" search in a singe file. This will confuse latex-suite. Set your grep
" program to alway generate a file-name.
set grepprg=grep\ -nH\ $*

" TIP: if you write your \label's as \label{fig:something}, then if you
" type in \ref{fig: and press you will automatically cycle through
" all the figure labels. Very useful!
set iskeyword+=:

" so .tex file will always be recognized as Latex.
let g:tex_flavor = "latex"
let g:Tex_UseMakefile = 0

""""""""""""""""""""newcomplcache""""""""""""""""""""""""""""
" Disable AutoComplPop.
let g:acp_enableAtStartup = 0
" Use neocomplcache.
let g:neocomplcache_enable_at_startup = 1
" Use smartcase.
let g:neocomplcache_enable_smart_case = 1
" Use camel case completion.
let g:neocomplcache_enable_camel_case_completion = 1
" Use underbar completion.
let g:neocomplcache_enable_underbar_completion = 1
" Set minimum syntax keyword length.
let g:neocomplcache_min_syntax_length = 3

" Enable omni completion.
autocmd FileType css setlocal omnifunc=csscomplete#CompleteCSS
autocmd FileType html,markdown setlocal omnifunc=htmlcomplete#CompleteTags
autocmd FileType javascript setlocal omnifunc=javascriptcomplete#CompleteJS
autocmd FileType python setlocal omnifunc=pythoncomplete#Complete
autocmd FileType xml setlocal omnifunc=xmlcomplete#CompleteTags

" Rainbow
let g:rainbow_active = 1
let g:rainbow_conf = {
\ 'ctermfgs': ['lightyellow', 'lightmagenta', 'lightblue', 'lightgreen', 'darkmagenta', 'darkblue', 'darkgreen', 'lightcyan', 'brown', 'lightred', 'darkcyan', 'darkred'],
\ 'guifgs': ['royalblue3', 'darkorange3', 'seagreen3', 'deeppink4', 'darkorchid3', 'yellow4', 'red3', 'dodgerblue']
}

" support supertab
imap neocomplcache#sources#snippets_complete#expandable() ? "(neocomplcache_snippets_expand)" : (pumvisible() ? "" : "")
smap (neocomplcache_snippets_jump)
inoremap neocomplcache#complete_common_string()

""""""""""""""""""""OtherPlugins""""""""""""""""""""""""""""
" stop unknow filtype message by NERDCommentor
let NERDShutUp=1

" filetype
au BufRead,BufNewFile *.clj setlocal filetype=clojure
au BufRead,BufNewFile *.cljs setlocal filetype=clojure
au BufRead,BufNewFile *.cljx setlocal filetype=clojure
au BufRead,BufNewFile Dockerfile setlocal filetype=Dockerfile

" airline
let g:airline#extensions#whitespace#enabled = 0
let g:airline_powerline_fonts = 1
let g:airline_theme='bubblegum'
let g:airline#extensions#default#section_truncate_width = {
\ 'b': 79,
\ 'x': 60,
\ 'y': 88,
\ 'z': 45,
\ }

[jdevera]

You have vundle installed in a directory called Vundle.vim but your plugin line says Plugin 'Vundle'.

This name mismatch makes vundle not recognise Vundle.vim as one of its managed plugins.

So change your vimrc to say Plugin 'Vundle.vim' and your problem will go away. Next time vundle will want to remove the old Vundle directory. Let it do it, you'll still have the Vundle.vim one with the real Vundle installation.