Eclipse no longer compiling my code

I know this is not an Eclipse forum, but I'm hoping somebody who uses Eclipse can help me with this issue. I am a real newbie with Eclipse, and I wrote a small client-server program just to learn on. Everything worked, I added some threading to it, and everything worked as well. Now all of a sudden I am getting a NoClassDefFoundError, and the code doesn't even compile anymore.
I'm sure it was something I changed, probably the classpath - as that is what would cause this problem, but I can't figure out what I could have changed? The code is exactly the same, I commented some stuff out and then uncommented them.
Also the strange thing is that when I go to the command line to compile the program, and run it, I get the same error message, it compiles but then it gives me that runtime error. So one would think that is not an Eclipse problem but rather a java problem, but then I created a super simple class, basically a hello world, and it compiled and ran fine. It's really frustrating, because I'm spending all this time on the IDE when I should be spending it on code.

I visited the elicpse forum and googled as much as I could, but didn't get anywhere, or get any responses. I was hoping somebody here who actually uses Eclipse, and I'm sure there are plenty, could give me some advice.
so I started messing with the -cp param and I did java -cp . [compiled class] in the command line and that worked. Which really just confuses me more. I mean what happend to cause this, everything was working fine in Eclipse, and then all of a sudden my project gets all screwed up. In addition, when I create a new project it works. I'm trying to find the difference to no avail. So again, if anybody has any insight in to how Eclipse organizes it's projects and/or some overview concept of the Eclipse model I would appreciate it. Thanks.

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    j org.metabrick.xbird.client.tools.CommandInvoker.main([Ljava/lang/String;)V+19
    v ~StubRoutines::call_stub
    --------------- P R O C E S S ---------------
    Java Threads: ( => current thread )
    0x48aa5000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=3636]
    0x48aa0800 JavaThread "CompilerThread0" daemon [_thread_blocked, id=4076]
    0x48a9e400 JavaThread "Attach Listener" daemon [_thread_blocked, id=3144]
    0x48aac400 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=2248]
    0x48a86c00 JavaThread "Finalizer" daemon [_thread_blocked, id=2664]
    0x48a82800 JavaThread "Reference Handler" daemon [_thread_blocked, id=2700]
    =>0x003f6800 JavaThread "main" [_thread_in_Java, id=2968]
    Other Threads:
    0x48a7f400 VMThread [id=4028]
    0x48aa6800 WatcherThread [id=3704]
    VM state:not at safepoint (normal execution)
    VM Mutex/Monitor currently owned by a thread: None
    Heap
    def new generation total 72576K, used 28616K [0x029d0000, 0x07890000, 0x07890000)
    eden space 64512K, 32% used [0x029d0000, 0x03e6fdd0, 0x068d0000)
    from space 8064K, 92% used [0x068d0000, 0x07022230, 0x070b0000)
    to space 8064K, 0% used [0x070b0000, 0x070b0000, 0x07890000)
    tenured generation total 967936K, used 253073K [0x07890000, 0x429d0000, 0x429d0000)
    the space 967936K, 26% used [0x07890000, 0x16fb4788, 0x16fb4800, 0x429d0000)
    compacting perm gen total 12288K, used 5879K [0x429d0000, 0x435d0000, 0x469d0000)
    the space 12288K, 47% used [0x429d0000, 0x42f8dd08, 0x42f8de00, 0x435d0000)
    No shared spaces configured.
    Dynamic libraries:
    0x00400000 - 0x00423000      C:\Program Files\Java\jdk1.6.0\bin\javaw.exe
    0x7c940000 - 0x7c9dd000      C:\WINDOWS\system32\ntdll.dll
    0x7c800000 - 0x7c931000      C:\WINDOWS\system32\kernel32.dll
    0x77d80000 - 0x77e29000      C:\WINDOWS\system32\ADVAPI32.dll
    0x77e30000 - 0x77ec1000      C:\WINDOWS\system32\RPCRT4.dll
    0x77cf0000 - 0x77d7f000      C:\WINDOWS\system32\USER32.dll
    0x77ed0000 - 0x77f17000      C:\WINDOWS\system32\GDI32.dll
    0x762e0000 - 0x762fd000      C:\WINDOWS\system32\IMM32.DLL
    0x60740000 - 0x60749000      C:\WINDOWS\system32\LPK.DLL
    0x73f80000 - 0x73feb000      C:\WINDOWS\system32\USP10.dll
    0x77bc0000 - 0x77c18000      C:\WINDOWS\system32\msvcrt.dll
    0x7c340000 - 0x7c396000      C:\Program Files\Java\jdk1.6.0\jre\bin\msvcr71.dll
    0x6d7f0000 - 0x6da2f000      C:\Program Files\Java\jdk1.6.0\jre\bin\client\jvm.dll
    0x76af0000 - 0x76b1b000      C:\WINDOWS\system32\WINMM.dll
    0x6d310000 - 0x6d318000      C:\Program Files\Java\jdk1.6.0\jre\bin\hpi.dll
    0x76ba0000 - 0x76bab000      C:\WINDOWS\system32\PSAPI.DLL
    0x6d7a0000 - 0x6d7ac000      C:\Program Files\Java\jdk1.6.0\jre\bin\verify.dll
    0x6d3a0000 - 0x6d3bf000      C:\Program Files\Java\jdk1.6.0\jre\bin\java.dll
    0x6d7e0000 - 0x6d7ef000      C:\Program Files\Java\jdk1.6.0\jre\bin\zip.dll
    0x6d560000 - 0x6d573000      C:\Program Files\Java\jdk1.6.0\jre\bin\net.dll
    0x719e0000 - 0x719f7000      C:\WINDOWS\system32\WS2_32.dll
    0x719d0000 - 0x719d8000      C:\WINDOWS\system32\WS2HELP.dll
    0x6d580000 - 0x6d589000      C:\Program Files\Java\jdk1.6.0\jre\bin\nio.dll
    VM Arguments:
    jvm_args: -Xmx1024m -Xms1024m
    java_command: org.metabrick.xbird.client.tools.CommandInvoker -col /xmark import document C:\Software\xmark\xmark100.xml
    Launcher Type: SUN_STANDARD
    Environment Variables:
    JAVA_HOME=C:\Program Files\Java\jdk1.6.0
    PATH=C:\Program Files\Java\jdk1.6.0\bin;D:\Software\maven-1.0.2\bin;D:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;D:\Software\apache-ant-1.6.5\bin;C:\ghc\ghc-6.4.2\bin;C:\Program Files\QuickTime\QTSystem\
    USERNAME=yui
    OS=Windows_NT
    PROCESSOR_IDENTIFIER=x86 Family 15 Model 4 Stepping 4, GenuineIntel
    --------------- S Y S T E M ---------------
    OS: Windows XP Build 2600 Service Pack 2
    CPU:total 2 family 15, cmov, cx8, fxsr, mmx, sse, sse2, ht
    Memory: 4k page, physical 2096404k(108924k free), swap 3511144k(1471688k free)
    vm_info: Java HotSpot(TM) Client VM (1.6.0-beta2-b86) for windows-x86, built on Jun 2 2006 00:36:31 by "java_re" with unknown MS VC++:1310

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    # J org.metabrick.xbird.util.collections.Int2LongHash$Int2LongLRUMap$ChainedEntry.recordRemoval(Lorg/metabrick/xbird/util/collections/Int2LongHash;)V
    --------------- T H R E A D ---------------
    Current thread (0x00036190): JavaThread "main" [_thread_in_Java, id=1608]
    siginfo: ExceptionCode=0xc0000005, writing address 0xfa424094
    Registers:
    EAX=0x00040e40, EBX=0xfa424078, ECX=0x05bd3fc0, EDX=0x05bd3fc0
    ESP=0x0007f578, EBP=0x0007f590, ESI=0xfa424078, EDI=0x081c8168
    EIP=0x00b8c9f8, EFLAGS=0x00010203
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    0x0007f578: 081c1fa8 6d7d1061 022dd1c8 00000000
    0x0007f588: 00000200 00000200 0007f5c8 00b8c598
    0x0007f598: 0899f428 05bd3fc0 00000200 00000000
    0x0007f5a8: 0007f5c8 00b41018 00000200 000001cb
    0x0007f5b8: 05c50338 05c19448 05bd3fc0 000001a8
    0x0007f5c8: 0007f648 00b8b880 07dd565c 0899f428
    0x0007f5d8: 022dd1cb 00000000 08976190 00b8054c
    0x0007f5e8: 00001000 0000af89 00001000 6d7d1061
    Instructions: (pc=0x00b8c9f8)
    0x00b8c9e8: 89 5f 20 c1 e8 09 c6 80 00 a9 6c 48 00 8b 72 20
    0x00b8c9f8: 89 7e 1c c1 ee 09 c6 86 00 a9 6c 48 00 8b e5 5d
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    Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
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    J org.metabrick.xbird.util.collections.Int2LongHash.remove(I)J
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    J com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanEndElement()I
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    j com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Z)Z+24
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    j com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Lcom/sun/org/apache/xerces/internal/xni/parser/XMLInputSource;)V+29
    j com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Lcom/sun/org/apache/xerces/internal/xni/parser/XMLInputSource;)V+9
    j com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Lorg/xml/sax/InputSource;)V+43
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    j org.metabrick.xbird.client.tools.CommandInvoker.executeCommand([Ljava/lang/String;)Z+8
    j org.metabrick.xbird.client.tools.CommandInvoker.run([Ljava/lang/String;)V+66
    j org.metabrick.xbird.client.tools.CommandInvoker.main([Ljava/lang/String;)V+19
    v ~StubRoutines::call_stub
    V [jvm.dll+0x845a9]
    V [jvm.dll+0xd9317]
    V [jvm.dll+0x8447a]
    V [jvm.dll+0x8b44a]
    C [java.exe+0x14c5]
    C [java.exe+0x64dd]
    C [kernel32.dll+0x16fd7]
    --------------- P R O C E S S ---------------
    Java Threads: ( => current thread )
    0x00aa7490 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=1780]
    0x00aa60f0 JavaThread "CompilerThread0" daemon [_thread_blocked, id=3456]
    0x00aa53f8 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=2544]
    0x00a96c80 JavaThread "Finalizer" daemon [_thread_blocked, id=856]
    0x00a957e8 JavaThread "Reference Handler" daemon [_thread_blocked, id=816]
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    def new generation total 72576K, used 59965K [0x02ae0000, 0x079a0000, 0x079a0000)
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    from space 8064K, 99% used [0x069e0000, 0x071bfff8, 0x071c0000)
    to space 8064K, 0% used [0x071c0000, 0x071c0000, 0x079a0000)
    tenured generation total 967936K, used 451270K [0x079a0000, 0x42ae0000, 0x42ae0000)
    the space 967936K, 46% used [0x079a0000, 0x23251ab0, 0x23251c00, 0x42ae0000)
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    0x00400000 - 0x0040c000      C:\Program Files\Java\jdk1.5.0_06\bin\java.exe
    0x7c940000 - 0x7c9dd000      C:\WINDOWS\system32\ntdll.dll
    0x7c800000 - 0x7c931000      C:\WINDOWS\system32\kernel32.dll
    0x77d80000 - 0x77e29000      C:\WINDOWS\system32\ADVAPI32.dll
    0x77e30000 - 0x77ec1000      C:\WINDOWS\system32\RPCRT4.dll
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    0x76af0000 - 0x76b1b000      C:\WINDOWS\system32\WINMM.dll
    0x762e0000 - 0x762fd000      C:\WINDOWS\system32\IMM32.DLL
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    0x6d6b0000 - 0x6d6bc000      C:\Program Files\Java\jdk1.5.0_06\jre\bin\verify.dll
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    PATH=C:\Program Files\Java\jdk1.6.0\bin;D:\Software\maven-1.0.2\bin;D:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;D:\Software\apache-ant-1.6.5\bin;C:\ghc\ghc-6.4.2\bin;C:\Program Files\QuickTime\QTSystem\
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    --------------- S Y S T E M ---------------
    OS: Windows XP Build 2600 Service Pack 2
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