I just finished a draft paper on the dynamic relationship between the Army and Islamic groups in Indonesia. I compared the nature of the relationship in the period of transition to authoritarian rule in the 1950s and the period of transition to democracy in in the 1990s.
The draft paper (in pdf format) is downloadable at the website of The Interseksi Foundation (click here). I helped the founding of the Interseksi Foundation and am a member of it, aside from my affiliation with CSIS in Jakarta.
I am enthusiastically waiting for comments and criticisms to the paper.