As is common with many works in progress, we have only had time to comment the source as it has evolved. We plan to provide more documentation in the future. Jikes TM is a research project, providing just the core function of Java compilation. It is not an IBM product, and is certainly not a replacement for, or alternative to, IBM products such as VAJava. The latter is a full, industrial-strength product.
Compilation is but one of the many functions that it provides.
Jikes is a source to bytecode compiler, and not a bytecode to native compiler, such as the High Performance Java compiler that is part of the latest VisualAge Product. Thus it is possible that Jikes may reject a program that another IBM-written compiler accepts, or vice versa.