This should be a very straightforward problem.  I have a simple .vimrc file.  It is 15 lines in its entirety:
filetype off
set nocompatible
call pathogen#infect()
syntax on
filetype plugin indent on
set hlsearch
set colorcolumn=79
set number
set list
set expandtab
set tabstop=4
set softtabstop=4
colorscheme vividchalk
When I try to start vim, though, I get the following error message:
Error detected while processing /Users/Jon/.vimrc:
line    3:
E117: Unknown function: pathogen#infect
line   15:
E185: Cannot find color scheme 'vividchalk'
I have worked quite a while at solving this, including looking here: Vim: Pathogen not loading and here: Pathogen does not load plugins and here: https://github.com/tpope/vim-pathogen/issues/50
I am storing all my vim-related files in a ~/.dotfiles/vim/ directory and have symlinked .vimrc and .gvimrc and .vim/from my home directory.  I have three plugins I am trying to load: command-t, commentary, and fugitive.  These plugins are all git submodules.  The directory structure is as follows:
.dotfiles/
 ├──vim/
    ├── autoload/
    │   └── pathogen.vim
    ├── bundle/
    │   ├── command-t/
    │   ├── commentary/
    │   └── fugitive/
    ├── colors/
    │   ├── distinguished.vim
    │   └── vividchalk.vim
    ├── ftdetect/
    │   ├── markdown.vim
    │   └── vim.vim
    ├── gvimrc
    ├── snippets/
    │   └── markdown.snippets
    ├── syntax/
    │   ├── markdown.vim
    │   └── python.vim
    ├── test.txt
    └── vimrc
 
     
     
     
    