Turns out gofmt doesn't actually return 1 when it finds problems, only when it finds source files which don't compile (all of which are now excluded).
This also fixes existing overlooked inconsistencies as a result of this mistake.
Previously they were roots, with children hanging off them. Now they are children of Files, and both CommentGroups and Comments can be discovered using AstNode.getAChild.
The PrintAst pass is also adapted to account for their new position.