I must have been typing something incorrectly. I was able to get it to work.
Given,
src/main/resources/shiro/definitions
-- shiro.stg
src/main/resources/shiro/definitions/test
-- decl.st
-- init.st
I can access the templates as a folder with:
STGroup group = new STGroupDir("shiro/definitions/test");
ST st = group.getInstanceOf("decl");
I can access the group file with:
STGroup group = new STGroupFile("shiro/definitions/shiro.stg");
ST st = group.getInstanceOf("decl");
It works!