About ten years ago I've made an Indonesian stemmer for my workplace. I'll try to find the code and refresh my memory again.
Topic on User talk:TJones (WMF)/Notes/Analysis of Applying Indonesian Analysis Chain to Malay
I saw your link to Github. Your stemmer looks a lot more complex than the Lucene one, so I'm guessing it does a better job, too. For now, though, I think having the Indonesian projects and Malay projects use the same stemmer makes sense, and we could look at upgrading them both in the future if you think your stemmer could do a better job.