call pathogen#runtime_append_all_bundles()
is not needed at all: the function is deprecated and not useful anyway.
If you really need to be safe, this is what you should have at the top of your ~/.vimrc
:
" turn filetype detection off and, even if it's not strictly
" necessary, disable loading of indent scripts and filetype plugins
filetype off
filetype plugin indent off
" pathogen runntime injection and help indexing
call pathogen#infect()
call pathogen#helptags()
" turn filetype detection, indent scripts and filetype plugins on
" and syntax highlighting too
filetype plugin indent on
syntax on
However, I've had the following for quite a while without any noticeable issue:
call pathogen#infect()
call pathogen#helptags()
filetype plugin indent on
syntax on