Let's say I got this plugin that's just messing my editor up all day and I want to disable it. Because pathogen just looks at the plugins dir and loads whatever is there I can't just remove it from a manifest (or something similar).
There IS though a cool global vimscript var called
g:pathogen_disabled that can be populated with all the vimscripts you'd like to disable.
It must be declared and populated before the call to
let g:pathogen_disabled =  call add(g:pathogen_disabled, 'vim-badplugin') call pathogen#infect()
There ya go! Now
vim-badplugin will not be included by pathogen!