Please provide a wrapping file manager, for example:

class WrappingJavaFileManager implements JavaFileManager {
    /** all calls are forwarded to this file manager */
    protected final JavaFileManager fileManager;
    protected FileObject wrap(FileObject fo) { return fo; }
    protected FileObject unwrap(FileObject fo) { return fo; }

    public FileObject getFileForInput(JavaFileManager.Location location, String packageName, URI relativeName) {
        return wrap(fileManager.getFileForInput(location, packageName, relativeName));
    }
    public String inferBinaryName(JavaFileManager.Location location, JavaFileObject file) {
        return fileManager.inferBinaryName(location, unwrap(file));
    }
    ...
}