here's output from my terminal while doing some commands right after
having started a new project from svn using subclipse and
the guidelines in the new programmer's guide.
peter@ubustu:~$ cd svn/JSynthLib/
peter@ubustu:~/svn/JSynthLib$  javadoc -locale en_US -breakiterator -quiet -d doc/api_docs -use -author -version -overview doc/programming.html core/*.java
Creating destination directory: "doc/api_docs/"
peter@ubustu:~/svn/JSynthLib$ java core/DeviceListWriter
Exception in thread "main" java.lang.NoClassDefFoundError: core/DeviceListWriter
Caused by: java.lang.ClassNotFoundException: core.DeviceListWriter
    at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336)
Could not find the main class: core/DeviceListWriter. Program will exit.
peter@ubustu:~/svn/JSynthLib$ ls
build.properties  ChangeLog  core  groovy.jar  jdom.jar        license.txt  makefile.vars  midiprovider  org     synthdrivers
build.xml         com        doc   images      JSynthLib.java  Makefile     META-INF       misc          README  synthdrivers.properties
peter@ubustu:~/svn/JSynthLib$ cd core
peter@ubustu:~/svn/JSynthLib/core$ ls
AbstractLibraryFrame.java  DeviceAddDialog.java       IBankPatch.java          MacUtils.java                PatchNameWidget.java         SysexGetDialog.java
Actions.java               DeviceDescriptor.java      IConverter.java          MidiConfigPanel.java         PatchTransferHandler.java    SysexHandler.java
AppConfig.java             DeviceDetailsDialog.java   IDriver.java             MidiMonitor.java             PrefsDialog.java             SysexMatcher.java
BankDriver.java            Device.java                ImportAllDialog.java     MidiScan.java                ProxyImportHandler.java      SysexSender.java
BankEditorFrame.java       DeviceListWriter.java      ImportMidiFile.java      MidiTest.java                ReassignPatchDialog.java     SysexSendToDialog.java
BankPrinter.java           DevicesConfig.java         IPatchDriver.java        MidiUtil.java                RepositoryConfigPanel.java   SysexStoreDialog.java
Base64.java                DeviceSelectionTree.java   IPatch.java              NewPatchDialog.java          ScanUnkownReportDialog.java  SysexWidget.java
CheckBoxWidget.java        DirectoryConfigPanel.java  ISinglePatch.java        NibbleSysex.java             SceneFrame.java              TreeWidget.java
ClipboardUtil.java         DocumentationWindow.java   JSLDesktop.java          NoteChooserConfigPanel.java  Scene.java                   UploadPatchDialog.java
ColumnLayout.java          Driver.java                JSLFrameEvent.java       NotifyingException.java      ScrollBarLookupWidget.java   Utility.java
ComboBoxWidget.java        DriverUtil.java            JSLFrame.java            package.html                 ScrollBarWidget.java         VertScrollBarLookupWidget.java
CompatibleFileDialog.java  EnvelopeWidget.java        JSLFrameListener.java    ParamModel.java              SearchDialog.java            VertScrollBarWidget.java
ConfigPanel.java           ErrorDialog.form           JSLWindowMenu.java       PatchBasket.java             SortDialog.java              WaitDialog.java
Constants.java             ErrorDialog.java           KnobLookupWidget.java    PatchContainer.java          SpinnerWidget.java           XMLFileUtils.java
Converter.java             ErrorMsg.java              KnobWidget.java          PatchEdit.java               Storable.java
CrossBreedDialog.java      FaderBoxConfigPanel.java   LabelWidget.java         PatchEditorFrame.java        Storage.java
CrossBreeder.java          FolderDialog.java          LibraryFrame.java        PatchesAndScenes.java        SwingWorker.java
DevDrvPatchSelector.java   GeneralConfigPanel.java    LookupManufacturer.java  Patch.java                   SynthConfigPanel.java
peter@ubustu:~/svn/JSynthLib/core$ cd ..
peter@ubustu:~/svn/JSynthLib$ java core/DeviceListWriter.java
Exception in thread "main" java.lang.NoClassDefFoundError: core/DeviceListWriter/java
Caused by: java.lang.ClassNotFoundException: core.DeviceListWriter.java
    at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336)
Could not find the main class: core/DeviceListWriter.java. Program will exit.
peter@ubustu:~/svn/JSynthLib$ java JSynthLib
Exception in thread "main" java.lang.NoClassDefFoundError: JSynthLib
Caused by: java.lang.ClassNotFoundException: JSynthLib
    at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336)
Could not find the main class: JSynthLib. Program will exit.
peter@ubustu:~/svn/JSynthLib$

This is because I didn't compile the .java source files into .class binary files first.

Compiling is done this way:
For Linux & Mac:
    javac -classpath '.:groovy.jar' org/jsynthlib/*/*/*.java org/jsynthlib/*/*.java
    javac core/*.java
    javac synthdrivers/*/*/*.java synthdrivers/*/*.java
    javac *.java
For Windows:
    javac -classpath '.;groovy.jar' org/jsynthlib/*/*/*.java org/jsynthlib/*/*.java
    javac core/*.java
    javac synthdrivers/*/*/*.java synthdrivers/*/*.java
    javac *.java