You can give https://github.com/ersiner/osx-env-sync a try. It handles both command line and GUI apps from a single source and works withe the latest version of OS X (Yosemite).
You can use path substitutions and other shell tricks since what you write is regular bash script to be sourced by bash in the first place. No restrictions.. (Check osx-env-sync documentation and you'll understand how it achieves this.)
I answered a similar question here where you'll find more.