Moving Executable Jar Breaks App Save Function

I've been trying to deploy my desktop application as an executable jar file but I'm facing the following problem: Whenever I move the jar file from its original build location, my application becomes unable to write to its external files. I initially thought the problem was path related; however, when moved the app can still load data from these files.
 
The solution is probably simple but for some reasons I've yet to find it .
 
The app consists of a jar file and a folder named "files" containing text files (such as library.data) to which serialized objects are written.
 
I wouldn't be surprise if the problem has to do with the xml build file, but all modification I've tried so far have failed. If it is likely that it is the problem, I'll be happy to post a copy of it upon request.
 
public static void saveLibraryToFile() {
    File file = new File(System.getProperty("user.dir")+"fileslibrary.data");
    if (file != null && file.exists()) {
        library = new Library(sortedAccounts, accountCategoriesMap, accountCategoriesList);
 
[Code] ....
 
A mostly complete set of the relevant codes I'm using, including the full Ant xml file, can be found at : [URL] .....