Just wanted to mention Stow[1] here, which I use to symlink my dotfiles on a new machine on a per app basis for many years now. My set up script just installs basic compiler toolchain and runs a bunch of stow commands based on Linux/Mac OS. I also adhere to XDG base spec[2] so I can keep my ~/ clean.
Also, the latest version (>= 2.3.0, released June '19) has a new flag specific to managing dotfiles. When passing `--dotfiles`, stow replaces `dot-` at the beginning of filenames with `.` in the symlinks. The online help does not mention it, but the release notes and man pages do.
Yeah, I don't understand why people like reinventing the wheel, Stow works, Make works, both are available everywhere, you don't need 30 layers of JS to manage dotfiles, I'm not against progress, but at least make something better than what's already around.
I really like stow. It handles almost everything for me.
One thing, I didn't split things by apps per se. I split them based on task. In some machines, I do Python work, so I created a 'python' package. In some I do PHP, so I created a 'php' one. I have a 'base' one where it has my .bashrc, .profile, .bash_profile, fish configs and other things.
Everything in the .bashrc. .profile, etc is loaded around conditionals. So, while the files are long, the section only activates if the other package is available. I thought about splitting it onto files, but most editors have a way of collapsing sections, so I decided to keep it on one so it's easy to edit in one place.