Vim

To get started post-clone, you'll need to git submodule init followed by a git submodule update to pull in Vundle (required for bundle management). Once that's done, just open up vim and call :BundleInstall which will install all the configured bundles.

Mutt

The included settings for mutt don't actually reference any specific accounts, so you'll need to define, e.g.: folder, spoolfile, smtp_url and any other mailbox settings in a new configuration file under ~/.mutt and source it from your .muttrc.

.Xmodmap

The .Xmodmap file included is for use with a UK Apple USB keyboard. Mostly, it just puts things back where you would expect them to be (apart from Ins which I can't fix).

.oh-my-zsh

First, clone the upstream repo into $HOME:

git clone https://github.com/robbyrussell/oh-my-zsh.git ~/.oh-my-zsh

then just symlink everything from .oh-my-zsh/custom into ~/.oh-my-zsh/custom:

cd /path/to/dotfiles/checkout
ln -s $(pwd)/.oh-my-zsh/custom/* ~/.oh-my-zsh/custom