Historical record of file access?

I have some files/folders that are disappearing(or relocating) on my server. AFP logs give you a pretty good view of who accesses what and what they did. SMB seems about useless. What about shell access and such? Does anyone know how I can track this regardless of protocol or method? Is there a utility out there or perhaps some log I am overlooking?
-Thanks in advance...
-James

Thanks. Helped me to narrow it down some more, maybe. Fact is - I can't even create INSIDE the webapp:
String s = context.getRealPath("/WEB-INF/") + "newsave.txt";
     File outputfile = new File(s);
     if(!outputfile.exists()) {
          outputfile.createNewFile();
}without incurring...
java.io.IOException: Permission denied
     at java.io.UnixFileSystem.createFileExclusively(Native Method)
     at java.io.File.createNewFile(File.java:850)
     at EchoServlet.doPost(EchoServlet.java:80)
Does this mean I have permission issues? Or is there something more basic I'm missing? (Believe me, it could be basic!)

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