wizard4j offers a java engine that 'runs' flowcharts (written in xml). A 'flowchart run' creates a sequence of user interactions (java api, html forms, rs, ...).The result of a 'run' can be applied to template frameworks like Velocity or Freemarker
FAST(Flowchart Abstract Syntax Tree) SDK is a development toolkit built upon Eclipse RCP and GEF to visualize the process of converting unstructured flowcharts in to structured ones.