One of the tracked files in vim/bundle/pathogen has been modified somehow. There is also some untracked (and unignored) content in the submodule vim/bundle/sparkup. In either case, the way to figure out what is modified / untracked is to change into the submodule directory and run git status. (In the case of untracked files in a submodule, this is frequently a build product that has not been added to .gitignore in upstream.)