Shell environment variables not available in GUI apps even if app launched via Command Line It is expected that shell environment variables won't be available in GUI apps launched via Spotlight or Finder.app. 

But until Mavericks - I could launch an app via Command line such as:

open -a IntelliJ\ IDEA\ 11


And Intellij will inherit the environment variables defined in shell (In my case zsh). This does not seem to work properly anymore. I have seen similar problem, when I launch Emacs.app from command line.

Related thread -  https://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite

BTW, I know I can use Setting the system-wide PATH environment variable in Mavericks for setting system wide environment variables, but I don't want system wide environment variables. I want GUI app to inherit variables that were defined at the point, the app was launched from command line.
You can try something like this:

launchctl setenv VARIABLE VALUE
open -a IntelliJ\ IDEA\ 11
launchctl unsetenv VARIABLE


This will pass environment variable VARIABLE into the launched app and later it will be cleaned, but will remain in the app.