my .vim directory
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I symlink my ~/.vim directory to this repo. Similarly for ~/.vimrc and ~/.gvimrc.

All addons go in the bundle directory and are managed by Pathogen. Where possible they are installed as git submodules. For example:

git submodule add vim/bundle/vim-rooter

After a fresh clone of this repository, get the submodules with:

git submodule init
git submodule update

(See Git Submodules: Adding, Using, Removing, Updating for more information.)

If after call pathogen#helptags() you get a warning about a dirty submodule, add tags to bundle/REPO/.git/info/exclude, where REPO is the repository giving the warning.

Thanks to John MacFarlane for this tip.

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