Because we're trying to get this to release quickly some short cuts will be taken here. The files you're going to want are located in the source directory under pedro/plugins/.... . Some Java files have been included here to show you what they might look like: MassSpecExperimentLoader.java, PeakListAnalysis.java, PeakListExporter.java, and PeakListValidation.java. The main classes you'll have to be concerned with:
So let's say you want to create a data import plugin. You're going to create a subtree of new records of types X,Y,Z. You use the RecordModelFactory class to create blank versions of these record types. Then you interrogate the RecordModel, ListFieldModel and EditFieldModels to stuff data into the structures. At the end you invoke the NavigationTree's pasteNode method so it will appear in the tree.
Please take a look at the Java files, especially MassSpecExperimentLoader.java.