The tool of choice to perform deploy and management of dotfiles is thoughtbot's rcm. Assuming that you already have rcm installed on your system and this repository is cloned to your home directory, you can link all dotfiles to appropriate destinations with:
$ rcup
This will link all files presented here. Although you probably want to see what will be linked where and manually chose desired files:
$ lsrc # will list each file with its destination
$ rcup vimrc # will link `vimrc` from here to `~/.vimrc`
Vim section of my dotfiles ships with vim-plug plugin manager. List of plugins is available in vim/plugins.vim and sourced to vimrc.
I prefer to store specific areas of config in separate files rather then in vimrc. So vimrc has section in which each file from vim/config will be sourced into Vim via loop
As well as Vim, fish config comes with plugin manager of choice fisherman. So there is no need to manually install it. In the other hand, I believe shell plugins is a more private thing, so plugins are not included in current repository.
Take a look at gitconfig the first section of it has my name and email in it, so you don't really want to use it until you change or delete this section.