Staging a file skips Git filter "clean" actions?

Question

I have a Git filter set to do some tidy actions on XML files upon "clean" (meaning when added to the staged list of files to commit). If I do a "git add myfile.xml" from the command line, the "clean" filter fires, and the file that is staged is the tidied version. However, if I stage the file via Sourcetree's UI (in a "split view staging" mode), the file gets added to the staging area without being passed through the "clean" filter's setting.

How can I  get the git smudge/clean filters to fire when staging/checking out through the Sourcetree UI?

midnightlightning · Answer

But if this were PATH-related, wouldn't setting the "clean" filter to the absolute path to the script succeed? I did that and it still fails to do the filter through SourceTree.

Mikael Sandberg · Answer

Have a look at SRCTREE-3583. Sourcetree is most likely not picking up your script because it is launched as a service and will not pick up your changes to the PATH. You need to extend the PATH that your apps see, checkout http://stackoverflow.com/questions/25385934/setting-environment-variables-via-launchd-conf-no-longer-works-in-os-x-yosemite (mentioned in the issue) or search on how to extend PATH in OS X.

midnightlightning · Answer

You mean the script that runs as part of the "clean" filter? The "clean" filter I have currently set to "./myscript.sh", and the script file is in the root folder of the repo itself.

I tried changing the clean filter to "/absolute/path/to/my/repo/myscript.sh", but the same symptom remains; works when doing "git add" from the command line, but not when staging within SourceTree.