I think maybe you are trying to make this too difficult. But I have to ask a question or 2.
Are you having a problem with basic I/O in
JAVA or Is your problem with how to write to a file that exists inside a JAR file?
If the latter is true, then is your java program running from the same JAR file that the txt file exists? If this is true then just do your basic I/O for that file. A jar file is just a directory structure. So your applicaion will treat the files inside it just like any other file on the Hard Drive. For instance, if your JAR file is set up thusly:
classes/*.class
images/*.gif *.jpeg, etc
manafest
text/*.txt
Then you want to create a File object for a txt file:
File file = new File("/text/test.txt");
Now, if on the other hand your text files are contained outside of your app but still in a JAR file you will need to use a class Loader to get inside the JAR file and open them.
If you are having problems with Basic Java I/O I would suggest postsing some code you are using for your I/O operations and/or post a question in the Java I/O forum maybe.
Hope that helps a little.