Vim のインデントが正しく反映されない

Vim のインデントを 2 に設定していて
ファイルを操作している時は正しく反映されているように見えるのですが

GitHub 等で確認すると、その設定が正しく反映されていないようです。

Vim でのファイル操作時

GitHub での表示

~/.vimrc には以下のように記述しています。

set expandtab
set tabstop=2
set softtabstop=0
set shiftwidth=2
set autoindent
set smartindent

~/.vimrc 全体は以下のようになっています。

"*****************************************************************************
"" NeoBundle core
"*****************************************************************************

if has('vim_starting')
    set nocompatible               " Be iMproved

    " Required:
    set runtimepath+=~/.vim/bundle/neobundle.vim/
endif

let neobundle_readme=expand('~/.vim/bundle/neobundle.vim/README.md')

if !filereadable(neobundle_readme)
    echo "Installing NeoBundle..."
    echo ""
    silent !mkdir -p ~/.vim/bundle
    silent !git clone https://github.com/Shougo/neobundle.vim ~/.vim/bundle/neobundle.vim/
    let g:not_finsh_neobundle = "yes"

    " Run shell script if exist on custom select language

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/c/c.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/python/python.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/javascript/javascript.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/html/html.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/perl/perl.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/haskell/haskell.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/go/go.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/php/php.sh | bash -s stable

    silent !\curl -sSL https://raw.githubusercontent.com/avelino/vim-bootstrap/master/vim_template/langs/ruby/ruby.sh | bash -s stable

endif

" Required:
call neobundle#begin(expand('~/.vim/bundle/'))

" Let NeoBundle manage NeoBundle
" Required:
NeoBundleFetch 'Shougo/neobundle.vim'

"*****************************************************************************
"" NeoBundle install packages
"*****************************************************************************
NeoBundle 'scrooloose/nerdtree'
NeoBundle 'tpope/vim-commentary'
NeoBundle 'tpope/vim-fugitive'
NeoBundle 'tpope/vim-surround'
NeoBundle 'tomtom/tcomment_vim'
NeoBundle 'osyo-manga/vim-over'
NeoBundle 'ctrlpvim/ctrlp.vim'
NeoBundle 'LeafCage/yankround.vim'
NeoBundle 'kana/vim-submode'
NeoBundle 'bling/vim-airline'
NeoBundle 'airblade/vim-gitgutter'
NeoBundle 'sheerun/vim-polyglot'
NeoBundle 'vim-scripts/grep.vim'
NeoBundle 'vim-scripts/CSApprox'
NeoBundle 'bronson/vim-trailing-whitespace'
NeoBundle 'Shougo/neocomplete.vim'
NeoBundle 'Shougo/vimproc.vim', {
            \ 'build' : {
            \     'windows' : 'tools\\update-dll-mingw',
            \     'cygwin' : 'make -f make_cygwin.mak',
            \     'mac' : 'make -f make_mac.mak',
            \     'unix' : 'make -f make_unix.mak',
            \    },
            \ }
if v:version > 702
    NeoBundle 'Shougo/vimshell.vim'
endif

"" Vim-Session
NeoBundle 'xolox/vim-misc'
NeoBundle 'xolox/vim-session'

"" Snippets
NeoBundle 'SirVer/ultisnips'
NeoBundle 'honza/vim-snippets'

"" Color
NeoBundle 'tomasr/molokai'
NeoBundle 'vim-scripts/desertEx'
NeoBundle 'stulzer/heroku-colorscheme'
NeoBundle 'wellsjo/wells-colorscheme.vim'
NeoBundle 'farseer90718/flattr.vim'
NeoBundle 'ajh17/Spacegray.vim'
NeoBundle 'dsolstad/vim-wombat256i'
NeoBundle 'NLKNguyen/papercolor-theme'

"" Vim-Bootstrap Updater
NeoBundle 'sherzberg/vim-bootstrap-updater'

let g:vim_bootstrap_langs = "javascript,ruby,haskell,python,c,php,html,perl,go"
let g:vim_bootstrap_editor = "vim"              " nvim or vim

"" Custom bundles

NeoBundle 'vim-scripts/c.vim'
NeoBundle 'tyru/caw.vim.git'
NeoBundle 'Townk/vim-autoclose'
NeoBundleLazy 'tpope/vim-endwise', {
  \ 'autoload' : { 'insert' : 1, }}

"" Python Bundle
NeoBundle 'davidhalter/jedi-vim'
NeoBundle 'scrooloose/syntastic'
NeoBundle 'majutsushi/tagbar'
NeoBundle 'Yggdroot/indentLine'

"" Javascript Bundle
NeoBundle 'scrooloose/syntastic'
NeoBundle 'jelera/vim-javascript-syntax'
NeoBundle 'kchmck/vim-coffee-script'
NeoBundle 'moll/vim-node'
NeoBundle 'pangloss/vim-javascript'

"" HTML Bundle
NeoBundle 'amirh/HTML-AutoCloseTag'
NeoBundle 'alvan/vim-closetag'
NeoBundle 'hail2u/vim-css3-syntax'
NeoBundle 'gorodinskiy/vim-coloresque'
NeoBundle 'tpope/vim-haml'
NeoBundle 'mattn/emmet-vim'

NeoBundle 'vim-perl/vim-perl'
NeoBundle 'c9s/perlomni.vim'

NeoBundle "eagletmt/neco-ghc"
NeoBundle "dag/vim2hs"
NeoBundle "pbrisbin/vim-syntax-shakespeare"

"" Go Lang Bundle
NeoBundle "majutsushi/tagbar"
NeoBundle "fatih/vim-go"

"" PHP Bundle
NeoBundle 'arnaud-lb/vim-php-namespace'

"" Ruby Bundle
NeoBundle "tpope/vim-rails"
NeoBundle "tpope/vim-rake"
NeoBundle "tpope/vim-projectionist"
NeoBundle 'tpope/vim-endwise'
NeoBundle "thoughtbot/vim-rspec"
NeoBundle "majutsushi/tagbar"
NeoBundle 'scrooloose/syntastic'
NeoBundle 'marcus/rsense'
NeoBundle 'supermomonga/neocomplete-rsense.vim'

"" Include user's extra bundle
" if filereadable(expand("~/.vimrc.local.bundles"))
"   source ~/.vimrc.local.bundles
" endif

call neobundle#end()

" Required:
filetype plugin indent on

" If there are uninstalled bundles found on startup,
" this will conveniently prompt you to install them.
NeoBundleCheck

"*****************************************************************************
"" Basic Setup
"*****************************************************************************"
"" Encoding
set encoding=utf-8
set fileencoding=utf-8
set fileencodings=utf-8

"" Fix backspace indent
set backspace=indent,eol,start

"" Tabs. May be overriten by autocmd rules
set expandtab
set tabstop=2
set shiftwidth=2
set autoindent
set smartindent

"" Map leader to ,
let mapleader=','

"" Enable hidden buffers
set hidden

"" Searching
set hlsearch
set incsearch
set ignorecase
set smartcase

"" Encoding
set bomb
set binary
set ttyfast

"" Directories for swp files
set nobackup
set noswapfile

set fileformats=unix,dos,mac
set showcmd
set shell=/bin/sh

" session management
let g:session_directory = "~/.vim/session"
let g:session_autoload = "no"
let g:session_autosave = "no"
let g:session_command_aliases = 1

"*****************************************************************************
"" Visual Settings
"*****************************************************************************
syntax on
set ruler
set number

let no_buffers_menu=1
if !exists('g:not_finsh_neobundle')
    colorscheme molokai
endif

set cursorline
hi LineNr ctermfg=darkgray
set mousemodel=popup
set t_Co=256
set guioptions=egmrti
set gfn=Monospace\ 10

if has("gui_running")
    if has("gui_mac") || has("gui_macvim")
        set guifont=Inconsolata:h12
        set transparency=7
    endif
else
    let g:CSApprox_loaded = 1

    if $COLORTERM == 'gnome-terminal'
        set term=gnome-256color
    else
        if $TERM == 'xterm'
            set term=xterm-256color
        endif
    endif
endif

if &term =~ '256color'
    set t_ut=
endif

"" Disable the blinking cursor.
set gcr=a:blinkon0
set scrolloff=3

"" Status bar
set laststatus=2

"" Use modeline overrides
set modeline
set modelines=10

set title
set titleold="Terminal"
set titlestring=%F

set statusline=%F%m%r%h%w%=(%{&ff}/%Y)\ (line\ %l\/%L,\ col\ %c)\

if exists("*fugitive#statusline")
    set statusline+=%{fugitive#statusline()}
endif

" vim-airline
let g:airline_theme = 'molokai'
let g:airline#extensions#syntastic#enabled = 1
let g:airline#extensions#branch#enabled = 1
let g:airline#extensions#tabline#enabled = 1

if !exists('g:airline_symbols')
    let g:airline_symbols = {}
endif

if !exists('g:airline_powerline_fonts')
    let g:airline#extensions#tabline#left_sep = ' '
    let g:airline#extensions#tabline#left_alt_sep = '|'
else
    let g:airline#extensions#tabline#left_sep = ''
    let g:airline#extensions#tabline#left_alt_sep = ''

    " powerline symbols
    let g:airline_left_sep = ''
    let g:airline_left_alt_sep = ''
    let g:airline_right_sep = ''
    let g:airline_right_alt_sep = ''
    let g:airline_symbols.branch = ''
    let g:airline_symbols.readonly = ''
    let g:airline_symbols.linenr = ''
endif
"*****************************************************************************
"" Abbreviations
"*****************************************************************************
"" no one is really happy until you have this shortcuts
cnoreabbrev W! w!
cnoreabbrev Q! q!
cnoreabbrev Qall! qall!
cnoreabbrev Wq wq
cnoreabbrev Wa wa
cnoreabbrev wQ wq
cnoreabbrev WQ wq
cnoreabbrev W w
cnoreabbrev Q q
cnoreabbrev Qall qall

"" NERDTree configuration
let g:NERDTreeChDirMode=2
let g:NERDTreeIgnore=['\.rbc$', '\~$', '\.pyc$', '\.db$', '\.sqlite$', '__pycache__']
let g:NERDTreeSortOrder=['^__\.py$', '\/$', '*', '\.swp$', '\.bak$', '\~$']
let g:NERDTreeShowBookmarks=1
let g:nerdtree_tabs_focus_on_files=1
let g:NERDTreeMapOpenInTabSilent = '<RightMouse>'
let g:NERDTreeWinSize = 20
set wildignore+=*/tmp/*,*.so,*.swp,*.zip,*.pyc,*.db,*.sqlite
nnoremap <silent> <F2> :NERDTreeFind<CR>
nnoremap <C-e> :NERDTreeToggle<CR>

" grep.vim
nnoremap <silent> <leader>f :Rgrep<CR>
let Grep_Default_Options = '-IR'

" vimshell.vim
let g:vimshell_user_prompt = 'fnamemodify(getcwd(), ":~")'
let g:vimshell_prompt =  '$ '

" terminal emulation
if g:vim_bootstrap_editor == 'nvim'
    nnoremap <silent> <leader>sh :terminal<CR>
else
    nnoremap <silent> <leader>sh :VimShellCreate<CR>
endif

"*****************************************************************************
"" Functions
"*****************************************************************************
if !exists('*s:setupWrapping')
    function s:setupWrapping()
        set wrap
        set wm=2
        set textwidth=79
    endfunction
endif

"*****************************************************************************
"" Autocmd Rules
"*****************************************************************************
"" The PC is fast enough, do syntax highlight syncing from start
augroup vimrc-sync-fromstart
    autocmd!
    autocmd BufEnter * :syntax sync fromstart
augroup END

"" Remember cursor position
augroup vimrc-remember-cursor-position
    autocmd!
    autocmd BufReadPost * if line("'\"") > 1 && line("'\"") <= line("$") | exe "normal! g`\"" | endif
augroup END

"" txt
augroup vimrc-wrapping
    autocmd!
    autocmd BufRead,BufNewFile *.txt call s:setupWrapping()
augroup END

"" make/cmake
augroup vimrc-make-cmake
    autocmd!
    autocmd FileType make setlocal noexpandtab
    autocmd BufNewFile,BufRead CMakeLists.txt setlocal filetype=cmake
augroup END

set autoread

"*****************************************************************************
"" Mappings
"*****************************************************************************
"" Split
noremap <Leader>h :<C-u>split<CR>
noremap <Leader>v :<C-u>vsplit<CR>

"" Git
noremap <Leader>ga :Gwrite<CR>
noremap <Leader>gc :Gcommit<CR>
noremap <Leader>gsh :Gpush<CR>
noremap <Leader>gll :Gpull<CR>
noremap <Leader>gs :Gstatus<CR>
noremap <Leader>gb :Gblame<CR>
noremap <Leader>gd :Gvdiff<CR>
noremap <Leader>gr :Gremove<CR>

" session management
nnoremap <leader>so :OpenSession
nnoremap <leader>ss :SaveSession
nnoremap <leader>sd :DeleteSession<CR>
nnoremap <leader>sc :CloseSession<CR>

"" Tabs
nnoremap <Tab> gt
nnoremap <S-Tab> gT
nnoremap <silent> <S-t> :tabnew<CR>

"" Set working directory
nnoremap <leader>. :lcd %:p:h<CR>

"" Opens an edit command with the path of the currently edited file filled in
noremap <Leader>e :e <C-R>=expand("%:p:h") . "/" <CR>

"" Opens a tab edit command with the path of the currently edited file filled
noremap <Leader>te :tabe <C-R>=expand("%:p:h") . "/" <CR>

"" ctrlp.vim
set wildmode=list:longest,list:full
set wildignore+=*.o,*.obj,.git,*.rbc,*.pyc,__pycache__
let g:ctrlp_custom_ignore = '\v[\/]\.(git|hg|svn|tox)$'
let g:ctrlp_user_command = "find %s -type f | grep -Ev '"+ g:ctrlp_custom_ignore +"'"
let g:ctrlp_use_caching = 0
cnoremap <C-P> <C-R>=expand("%:p:h") . "/" <CR>
noremap <leader>b :CtrlPBuffer<CR>
let g:ctrlp_map = '<leader>e'
let g:ctrlp_open_new_file = 'r'

" snippets
let g:UltiSnipsExpandTrigger="<tab>"
let g:UltiSnipsJumpForwardTrigger="<tab>"
let g:UltiSnipsJumpBackwardTrigger="<c-b>"
let g:UltiSnipsEditSplit="vertical"

" syntastic
let g:syntastic_always_populate_loc_list=1
let g:syntastic_error_symbol='✗'
let g:syntastic_warning_symbol='⚠'
let g:syntastic_style_error_symbol = '✗'
let g:syntastic_style_warning_symbol = '⚠'
let g:syntastic_auto_loc_list=1
let g:syntastic_aggregate_errors = 1

"" Copy/Paste/Cut
if has('unnamedplus')
    set clipboard=unnamed,unnamedplus
endif

noremap YY "+y<CR>
noremap P "+gP<CR>
noremap XX "+x<CR>

if has('macunix')
    " pbcopy for OSX copy/paste
    vmap <C-x> :!pbcopy<CR>
    vmap <C-c> :w !pbcopy<CR><CR>
endif

"" Buffer nav
noremap <leader>z :bp<CR>
noremap <leader>q :bp<CR>
noremap <leader>x :bn<CR>
noremap <leader>w :bn<CR>

"" Close buffer
noremap <leader>c :bd<CR>

"" Clean search (highlight)
nnoremap <silent> <leader><space> :noh<cr>

"" Vmap for maintain Visual Mode after shifting > and <
vmap < <gv
vmap > >gv

"" Open current line on GitHub
noremap ,o :!echo `git url`/blob/`git rev-parse --abbrev-ref HEAD`/%\#L<C-R>=line('.')<CR> \| xargs open<CR><CR>

"" Custom configs

" Tagbar
nmap <silent> <F4> :TagbarToggle<CR>
let g:tagbar_autofocus = 1

" vim-python
augroup vimrc-python
    autocmd!
    autocmd FileType python setlocal expandtab shiftwidth=2 tabstop=2 colorcolumn=79
                \ formatoptions+=croq softtabstop=2 smartindent
                \ cinwords=if,elif,else,for,while,try,except,finally,def,class,with
augroup END

" jedi-vim
let g:jedi#popup_on_dot = 0
let g:jedi#goto_assignments_command = "<leader>g"
let g:jedi#goto_definitions_command = "<leader>d"
let g:jedi#documentation_command = "K"
let g:jedi#usages_command = "<leader>n"
let g:jedi#rename_command = "<leader>r"
let g:jedi#show_call_signatures = "0"
let g:jedi#completions_command = "<C-Space>"

" syntastic
let g:syntastic_python_checkers=['python', 'flake8']
let g:syntastic_python_flake8_post_args='--ignore=W391'

" vim-airline
let g:airline#extensions#virtualenv#enabled = 1
let g:airline#extensions#tagbar#enabled = 1

" Tagbar
nmap <silent> <F4> :TagbarToggle<CR>
let g:tagbar_autofocus = 1

let g:javascript_enable_domhtmlcss = 1

let g:haskell_conceal_wide = 1
let g:haskell_multiline_strings = 1
let g:necoghc_enable_detailed_browse = 1
autocmd Filetype haskell setlocal omnifunc=necoghc#omnifunc


" Tagbar
nmap <silent> <F4> :TagbarToggle<CR>
let g:tagbar_autofocus = 1

let g:tagbar_type_go = {
            \ 'ctagstype' : 'go',
            \ 'kinds'     : [  'p:package', 'i:imports:1', 'c:constants', 'v:variables',
            \ 't:types',  'n:interfaces', 'w:fields', 'e:embedded', 'm:methods',
            \ 'r:constructor', 'f:functions' ],
            \ 'sro' : '.',
            \ 'kind2scope' : { 't' : 'ctype', 'n' : 'ntype' },
            \ 'scope2kind' : { 'ctype' : 't', 'ntype' : 'n' },
            \ 'ctagsbin'  : 'gotags',
            \ 'ctagsargs' : '-sort -silent'
            \ }

let g:rubycomplete_buffer_loading = 1
let g:rubycomplete_classes_in_global = 1
let g:rubycomplete_rails = 1

augroup vimrc-ruby
    autocmd!
    autocmd BufNewFile,BufRead *.rb,*.rbw,*.gemspec setlocal filetype=ruby
    autocmd Filetype ruby setlocal tabstop=2 softtabstop=2 shiftwidth=2
augroup END

" Tagbar
nmap <silent> <F4> :TagbarToggle<CR>
let g:tagbar_autofocus = 1

let g:tagbar_type_ruby = {
            \ 'kinds' : [
            \ 'm:modules',
            \ 'c:classes',
            \ 'd:describes',
            \ 'C:contexts',
            \ 'f:methods',
            \ 'F:singleton methods'
            \ ]
            \ }

" emmet-vim
let g:user_emmet_settings = {
            \    'variables': {
            \      'lang': "ja"
            \    },
            \   'indentation': '  '
            \ }

" vim-gitgutter
let g:gitgutter_sign_added = '✚'
let g:gitgutter_sign_modified = '➜'
let g:gitgutter_sign_removed = '✘'

" Escape from INSERT MODE
inoremap <silent> jj <ESC>
inoremap <silent> <C-j> j
inoremap <silent> kk <ESC>

" neocomplete.vim
let g:acp_enableAtStartup = 0
let g:neocomplete#enable_at_startup = 1
let g:neocomplete#enable_smart_case = 1
if !exists('g:neocomplete#force_omni_input_patterns')
  let g:neocomplete#force_omni_input_patterns = {}
  endif
  let g:neocomplete#force_omni_input_patterns.ruby = '[^.*\t]\.\w*\|\h\w*::'

" Robocop
let g:syntastic_mode_map = { 'mode': 'passive', 'active_filetypes': ['ruby'] }
let g:syntastic_ruby_checkers = ['rubocop']

" Closure
imap " ""<Left>
imap ' ''<Left>

" Cursor movement in insert mode
inoremap <C-j> <Down>
inoremap <C-k> <Up>
inoremap <C-h> <Left>
inoremap <C-l> <Right>

" over.vim
nnoremap <silent> <Leader>m :OverCommandLine<CR>
nnoremap sub :OverCommandLine<CR>%s/<C-r><C-w>//g<Left><Left>
nnoremap subp y:OverCommandLine<CR>%s!<C-r>=substitute(@0, '!', '\\!', 'g')<CR>!!gI<Left><Left><Left>

" grep
autocmd QuickFixCmdPost *grep* cwindow

" Indent
let g:indentLine_faster = 1
nmap <silent><Leader>i :<C-u>IndentLinesToggle<CR>
set list listchars=tab:\¦\›

" Yank
nmap p <Plug>(yankround-p)
nmap P <Plug>(yankround-P)
nmap <C-p> <Plug>(yankround-prev)
nmap <C-n> <Plug>(yankround-next)
let g:yankround_max_history = 50
nnoremap <silent>g<C-p> :<C-u>CtrlPYankRound<CR>

" Paste
set clipboard+=unnamed

" Submode
call submode#enter_with('bufmove', 'n', '', 's>', '<C-w>>')
call submode#enter_with('bufmove', 'n', '', 's<', '<C-w><')
call submode#enter_with('bufmove', 'n', '', 's+', '<C-w>+')
call submode#enter_with('bufmove', 'n', '', 's-', '<C-w>-')
call submode#map('bufmove', 'n', '', '>', '<C-w>>')
call submode#map('bufmove', 'n', '', '<', '<C-w><')
call submode#map('bufmove', 'n', '', '+', '<C-w>+')
call submode#map('bufmove', 'n', '', '-', '<C-w>-')

" White Space
autocmd BufWritePre * :%s/\s\+$//ge

" Display of double-byte space
function! ZenkakuSpace()
    highlight ZenkakuSpace cterm=underline ctermfg=lightblue guibg=darkgray
endfunction

if has('syntax')
    augroup ZenkakuSpace
        autocmd!
        autocmd ColorScheme * call ZenkakuSpace()
        autocmd VimEnter,WinEnter,BufRead * let w:m1=matchadd('ZenkakuSpace', '　')
    augroup END
    call ZenkakuSpace()
endif

" HTML
let g:closetag_filenames = "*.html,*.xhtml,*.phtml,*.html.erb"

" JavaScript
au BufRead,BufNewFile jquery.*.js set ft=javascript syntax=jquery

以上です。
よろしくお願いします。

追記:

:set et? ts? sts? sw? の実行結果

noexpandtab
tabstop=2
softtabstop=0
shiftwidth=2

になります…！