Shotgun and wrapper scripts

Im kinda stumped here and looking for some insight into this.

We are running all of our applications with batch files now, where we set the env var and launch the app. (Windows)

We are trying to integrate Shotgun into the pipeline along with Shotgun Desktop so users can launch local file system files by clicking on a link the the web interface of shotgun.

Problem were having is if we go to the paths.yml file and adjust the maya.exe path to reflect the batch file, when you launch maya from shotgun desktop, it does not come up with the shotgun menu item.

Switch it back to the actual EXE, shows up just fine but without the env vars we need.

I read the documentation regarding the hooks and before app launch functions, but was curious if this is the only way to do it?

Id prefer it to launch via my batch files, so I dont have to update vars in multiple places project to project.

Any ideas?
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