Here is what I have. I have tried to remove ~/.vim/ftdetect ~/.vim/bundle-available ~/.vim/after ~/.vim/plugin.
The problem is not gone.
When I try to remove ~/.vim, the problem is gone.
It is very hard to debug this problem.
Could this problem be due to some interaction between two plugins?
$ cat ~/plugins.txt
1: /Applications/MacVim.app/Contents/Resources/vim/vimrc
2: ~/.vimrc
3: ~/.vim/autoload/pathogen.vim
4: ~/.vim/filetype.vim
5: /Applications/MacVim.app/Contents/Resources/vim/runtime/filetype.vim
6: ~/.vim/ftdetect/bug.vim
7: ~/.vim/ftdetect/json.vim
8: ~/.vim/ftdetect/markdown.vim
9: ~/.vim/ftdetect/sage.vim
10: ~/.vim/bundle-available/jade/ftdetect/jade.vim
11: ~/.vim/bundle-available/Nvim-R/ftdetect/r.vim
12: ~/.vim/bundle-available/R-Vim-runtime/ftdetect/r_file_types.vim
13: ~/.vim/bundle-available/vim-jq/ftdetect/jq.vim
14: ~/.vim/bundle-available/vim-jst/ftdetect/jst.vim
15: ~/.vim/bundle-available/vim-perl/ftdetect/mason-in-html.vim
16: ~/.vim/bundle-available/vim-perl/ftdetect/perl11.vim
17: ~/.vim/bundle-available/vim-racket/ftdetect/racket.vim
18: ~/.vim/bundle-available/vim-scala/ftdetect/scala.vim
19: ~/.vim/bundle-available/vim-solidity/ftdetect/solidity.vim
20: ~/.vim/after/filetype.vim
21: /Applications/MacVim.app/Contents/Resources/vim/runtime/ftplugin.vim
22: /Applications/MacVim.app/Contents/Resources/vim/runtime/indent.vim
23: /Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/syntax.vim
24: /Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/synload.vim
25: /Applications/MacVim.app/Contents/Resources/vim/runtime/syntax/syncolor.vim
26: ~/.vim/plugin/a.vim
27: ~/.vim/plugin/AnsiEscPlugin.vim
28: ~/.vim/plugin/cecutil.vim
29: ~/.vim/plugin/dbext.vim
30: ~/.vim/plugin/head.vim
31: ~/.vim/plugin/IndentAnything.vim
32: ~/.vim/plugin/LargeFile.vim
33: ~/.vim/plugin/matchit.vim
34: ~/.vim/plugin/pydoc.vim
35: ~/.vim/plugin/rails.vim
36: ~/.vim/plugin/screen.vim
37: ~/.vim/plugin/Tabular.vim
38: ~/.vim/plugin/vimim.vim
39: ~/.vim/bundle-available/cscope/plugin/cscope_maps.vim
40: ~/.vim/bundle-available/diffchar/plugin/diffchar.vim
41: ~/.vim/bundle-available/LanguageTool/plugin/LanguageTool.vim
42: ~/.vim/bundle-available/nerdtree/plugin/NERD_tree.vim
43: ~/.vim/bundle-available/nerdtree/autoload/nerdtree.vim
44: ~/.vim/bundle-available/nerdtree/lib/nerdtree/path.vim
45: ~/.vim/bundle-available/nerdtree/lib/nerdtree/menu_controller.vim
46: ~/.vim/bundle-available/nerdtree/lib/nerdtree/menu_item.vim
47: ~/.vim/bundle-available/nerdtree/lib/nerdtree/key_map.vim
48: ~/.vim/bundle-available/nerdtree/lib/nerdtree/bookmark.vim
49: ~/.vim/bundle-available/nerdtree/lib/nerdtree/tree_file_node.vim
50: ~/.vim/bundle-available/nerdtree/lib/nerdtree/tree_dir_node.vim
51: ~/.vim/bundle-available/nerdtree/lib/nerdtree/opener.vim
52: ~/.vim/bundle-available/nerdtree/lib/nerdtree/creator.vim
53: ~/.vim/bundle-available/nerdtree/lib/nerdtree/flag_set.vim
54: ~/.vim/bundle-available/nerdtree/lib/nerdtree/nerdtree.vim
55: ~/.vim/bundle-available/nerdtree/lib/nerdtree/ui.vim
56: ~/.vim/bundle-available/nerdtree/lib/nerdtree/event.vim
57: ~/.vim/bundle-available/nerdtree/lib/nerdtree/notifier.vim
58: ~/.vim/bundle-available/nerdtree/autoload/nerdtree/ui_glue.vim
59: ~/.vim/bundle-available/nerdtree/nerdtree_plugin/exec_menuitem.vim
60: ~/.vim/bundle-available/nerdtree/nerdtree_plugin/fs_menu.vim
61: ~/.vim/bundle-available/RST-Tables/plugin/rst_table.vim
62: ~/.vim/bundle-available/vim-cython/plugin/cython.vim
63: ~/.vim/bundle-available/vim-diff-enhanced/plugin/EnhancedDiff.vim
64: ~/.vim/bundle-available/vim-indent-guides/plugin/indent_guides.vim
65: ~/.vim/bundle-available/vim-indent-guides/autoload/indent_guides.vim
66: ~/.vim/bundle-available/vim-latex-suite/plugin/filebrowser.vim
67: ~/.vim/bundle-available/vim-latex-suite/plugin/imaps.vim
68: ~/.vim/bundle-available/vim-latex-suite/plugin/libList.vim
69: ~/.vim/bundle-available/vim-latex-suite/plugin/remoteOpen.vim
70: ~/.vim/bundle-available/vim-latex-suite/plugin/SyntaxFolds.vim
71: ~/.vim/bundle-available/vim-pandoc/plugin/pandoc.vim
72: ~/.vim/bundle-available/vim-pandoc-syntax/plugin/pandoc-syntax-check.vim
73: ~/.vim/bundle-available/vim-scala/plugin/scala.vim
74: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/getscriptPlugin.vim
75: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/gzip.vim
76: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/logiPat.vim
77: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/manpager.vim
78: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/matchparen.vim
79: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/netrwPlugin.vim
80: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/rrhelper.vim
81: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/spellfile.vim
82: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/tarPlugin.vim
83: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/tohtml.vim
84: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/vimballPlugin.vim
85: /Applications/MacVim.app/Contents/Resources/vim/runtime/plugin/zipPlugin.vim
86: ~/.vim/bundle-available/vim-pandoc-after/plugin/pandoc-after.vim