To compile the java classes you should check the classpath in the compile job. The compile job is in
<webapp_home>/webapps/<your website name>/web-inf/classes/src/openmodelling/tool. The job all.cmd compiles all the java classes.
Check compile.cmd for all the mentioned jar files (correct name, correct location).
Once this is done you can change the classes and compile, but remember to communicate your beautiful enhancements to Open Modeling (open source!).
If you want something but don't know where to begin just do a Support request.
We will help you!