Dear Shawon,
I was almost sure we had that (and even our config docs described it).
The configuration for hierarchical relations indeed worked, but was not making it to the annotation UI.
I just reworked the arc form so that the hierarchical relationships are displayed properly.
Please update your brat to the newest `master` from github.
Then, all you need to do is indent the relationship definitions in `annotation.conf` using Tab:
[relations]
RelType1 Arg1:Entity, Arg2:Entity
RelType1Agree Arg1:Entity, Arg2:Entity
RelType1Disagree Arg1:Entity, Arg2:Entity
RelType2 Arg1:Entity, Arg2:Entity
RelType2Agree Arg1:Entity, Arg2:Entity
RelType2Disagree Arg1:Entity, Arg2:Entity
Goran