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You should keep this repo in the root of your home directory ~/dotfiles.
Each folder, for example xorg/ represents a group of related configs (I like to sort them by app, but you can group them by computer, distro, etc).
Inside the group files should keep the original directory tree and filenames.
You will need GNU Stow to manage your configs (Archlinux: community/stow).
If there is no group for the new config, you should create a new folder.
Paste the config in is folder.
Examples:
[~/dotfiles]$ cp -r --parents /etc/pacman.conf pacman/
[~]$ cp -r --parents .config/ncmpcpp/ dotfiles/ncmpcpp/
If you don't know the meaning of the above command check man cp.
I recommend using Stow to farm the symlinks (read man stow).
By default the stow command will create symlinks for files in the parent directory of where you execute the command. So, assuming this repo is located at ~/dotfiles and all the following commands are executed in that directory (otherwise you should checkout the flags -d and -t using man stow).
Suppose you want to install vim and bash, you simply do:
stow -v vim bash
and this will create all symlinks, otherwise stow will tell you why it couldn't create them (normally you have to delete some files that are in the place were the symlinks should go).
To install a config that doesn't reside in the ~, for example the pacman config, you do:
stow -vt / pacman
Or if you want to install a config in /root, you do:
stow -vt /root vim
If you want to switch configs (for examples, if you have 2 vim configs, named vim-min, and vim):
stow -vD vim-min
stow -v vim
To finish, if you added a file to group and want to upgrade the symlinks without manually removing the instalation with -D and then installing again, you can use:
stow -vR vim
Please report any issues and suggestions. Thank you