I use gnu stow (with --no-folding) and track my stow directory in a Git repo. This allows you to easily swap out distro specific differences, like the location of git_prompt.sh or aliases that map to different package managers. Also, you can switch between different window managers or desktop environments with a simple unstow and stow of .xinitrc files.
Why do you need cross platform availability, if .desktop files are (mostly) Linux only?