I've probably spent hundreds of hours across all my configs over the years. In the old days, I'd rsync config files manually. Having frustrating times where I had to start everything over again.
I have a lot to say on the subject.
1. Like other users here, git is a great way version your files. Not just that, it handles the issue you have with keeping the configs of various systems in sync.
1b. It doesn't have to be GitHub, but understand pushing to some remote gives you a backup, and a way to keep the latest configs you have in sync across multiple machines.
2. As a rule of thumb, the more POSIX compliant you are, the more cross-compatible your dot-configs will be. In my case, a great deal of my config works superbly across Ubuntu, FreeBSD and OS X with no modification whatsoever.
4. Tangentially related is PATH's. Definitely be sure you're not accidentally appending multiple one's over again or omitting ones you want to search. For this, I recommend a pathappend function like one used at http://superuser.com/a/753948.
5. As for managing vim / neovim, I'm coming to the realization the amount of time I've spent trying to configure completion / fix tiny things over the years probably makes me lose the net benefit vim has given me. Too bad there is no intellij for the CLI. In any event, I keep a vim config at https://github.com/tony/vim-config which I document extensively. It has quite a lot of bells and whistles, but lazy loads and checks the system before installing certain plugins. It should work with neovim too.
I keep my central dot-configs (along with its submodules) at https://github.com/tony/.dot-config. Its permissively licensed, so feel free to copy whatever you'd like.
I have a lot to say on the subject.
1. Like other users here, git is a great way version your files. Not just that, it handles the issue you have with keeping the configs of various systems in sync.
1b. It doesn't have to be GitHub, but understand pushing to some remote gives you a backup, and a way to keep the latest configs you have in sync across multiple machines.
2. As a rule of thumb, the more POSIX compliant you are, the more cross-compatible your dot-configs will be. In my case, a great deal of my config works superbly across Ubuntu, FreeBSD and OS X with no modification whatsoever.
3. dotfiles (https://pypi.python.org/pypi/dotfiles) is very helpful for building those initial symlinks.
4. Tangentially related is PATH's. Definitely be sure you're not accidentally appending multiple one's over again or omitting ones you want to search. For this, I recommend a pathappend function like one used at http://superuser.com/a/753948.
5. As for managing vim / neovim, I'm coming to the realization the amount of time I've spent trying to configure completion / fix tiny things over the years probably makes me lose the net benefit vim has given me. Too bad there is no intellij for the CLI. In any event, I keep a vim config at https://github.com/tony/vim-config which I document extensively. It has quite a lot of bells and whistles, but lazy loads and checks the system before installing certain plugins. It should work with neovim too.
I keep my central dot-configs (along with its submodules) at https://github.com/tony/.dot-config. Its permissively licensed, so feel free to copy whatever you'd like.