I think it could be worth thinking about setting up a code formatting and checking system. There are a couple of Eclipse plugins, CheckStyle and PMD, that help doing so. CheckStyle (http://checkstyle.sourceforge.net/), as its name stands, checks the code style. It also allows to export an XML file with the desired settings, so all the people involved in a project could use the same settings. On the other hand, PMD (http://pmd.sourceforge.net/) is a source code analyzer that seeks a number of potential problems.
A less feasible proposal is to use Intent (http://www.eclipse.org/projects/project-plan.php?planurl=/intent/pages/plan/plan.xml) to implement a better documentation in OpenMarkov. Also, I need to say I have not been able to look to it thoroughly, so this part of the proposal needs a further and deeper look. But I think it was worth mentioning.