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The function

f :: Eq (a Bool Bool) => a Bool Bool -> a Bool Bool -> Bool
f = (==)

should be accepted by PAKCS, but the following error message is reported:

    Illegal class constraint Eq (a Bool Bool)
    Constraints must be of the form C u or C (u t1 ... tn),
    where C is a type class, u is a type variable and t1, ..., tn are types.
   |
 1 | f :: Eq (a Bool Bool) => a Bool Bool -> a Bool Bool -> Bool
   |      ^^

This error is caused by the function rootType, which is a subfunction of checkConstraint:

checkConstraint :: Constraint -> TSCM Constraint
checkConstraint c@(Constraint spi qcls ty) = do
  checkClass False qcls
  ty' <- checkType ty
  unless (isVariableType $ rootType ty') $ report $ errIllegalConstraint c
  return $ Constraint spi qcls ty'
  where
    rootType (ApplyType _ ty' _) = ty'
    rootType ty'                 = ty'

rootType is not defined recursively and only removes a single ApplyType, which means that type variables that are applied to multiple types are not identified as type variables. For example, a Bool Bool is represented in the AST by ApplyType (ApplyType (VariableType "a") (ConstructorType "Bool")) (ConstructorType "Bool") (simplified), so rootType returns ApplyType (VariableType "a") (ConstructorType "Bool"), which is not identified as a type variable by isVariableType.