Fresh Vim install, Vim permission errors, Vundle not functional
It's unclear to me how the owner of ~/.vim got set to root but Vundle will definitely have trouble updating packages if that is the case.
If I understand correctly, in that you now have Vim installed how you want it, I suggest redoing the customization process.
Move ~/.vim (for reference) and create the bundle directory where Vundle will be installed:
$ sudo mv ~/.vim ~/OLDvim
$ mkdir -p ~/.vim/bundle
This should now be an empty dir owned by your user.
Reinstall Vundle
$ git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim
Make sure you have the required lines in your ~/.vimrc,
- open vim and
- run
:BundleInstall
Once you got it working and you're happy with everything, you can rm -rf ~/OLDvim.
Changing the ownership of the .vim files to my username instead of root worked for me (did for all files recursively):
chown -R <username>:<username> .vim
Here's more info about chown.
Note: It seems like the reinstall answer would work too (though didn't end up trying it), but with the chown approach you don't have to do the reinstall steps.