I'm into a quite strange position (from my java-newbie point of view):
using Eclipse I wrote a "java program" (some .java files with classes into) which essentially (batch) reads a text *.csv file, "evaluates" its contents, and writes out results into an *_out.csv text file. To locate the input file it uses a "file chooser" (got sample from here: http://docs.oracle.com/javase/tutorial/uiswing/components/filechooser.html)
I debugged all the code and, using the debugger, it works.
I ran the code (the main class, which calls all the other in sequence) and it works, while in Eclipse.
I exported all the project's contents into a "runnable jar" file.
Notice that, file chooser apart, this is mainly a "batch" which reads and writes: nearly no User Interface at all. While into Eclipse I shown some internal results using something like "if(debug) System.out.print("something to print");" providing to set "debug" TRUE while debugging and FALSE while in production environment.
ALL of the above worked!
Now, starting the runnable jar (double-click on the jar file, in Win/XP), I can see the file chooser and I can use it but, after choosing the input file... nothing more: (having no user interface) I don't know if the file was read, I don't see any generated output file, and I've even no "console" to list any intermediate debug message, to see if the jar is working, even if I re-export it with the debug variable set to TRUE.
Is there a way to "runtime debug" the running jar (like VB's MsgBox, or something other)? some kind of "log file" I can "enable" or look into? (obviously, as my jar is not writing the result file, I just can't try writing a *.log too) I have also to say I just can't install other than Eclipse on my machine (and just been lucky it ran), so no usual developer's tools, utilities and other useful things.
Even though it is a runnable jar, you can still run it from a console -- open a terminal window, navigate to the directory containing the jar, and enter "java -jar yourJar.jar". It will run in that terminal window, and sysout and syserr output will appear there, including stack traces from uncaught exceptions. Be sure to have your debug set to true when you compile. And good luck.
Just thought of something else -- if you're on Win7, it often has permission problems with user applications writing files to specific directories. Make sure the directory to which you are writing your output file is one for which you have permissions.
In a future project, if it's big enough, you can use one of the standard logging facilities for 'debug' output; then it will be easy(ier) to redirect it to a file instead of depending on having a console. But for a smaller job like this, this should be fine.