Use Relative Path In Place Of Absolute Path

I am copying the xml files from one folder to other folder, in the source folder, i have some files which have some content like "backing File="$IDP_ ROOT/metadata/iPAU-SP-metadata.xml" but while writing to the destination folder.i am replacing the "$IDP_ROOT" with my current working directory. The entire copying of files is for deploying into tomcat server. The copying is done only when server starts for the first time.Problem: If i change the folder name from my root path in my machine after i run the server,the entire process will be stopped because the destination folder files already contains the content which is with existed files names or folder names.

So i want to change it to relative path instead absolute path. What is the best way to do it? Please look at code below:

[ // Getting the current working directory
String currentdir = new File(".").getAbsoluteFile().getParent() + File.separator;

if(currentdir.indexOf("ControlPanel")!=-1){
rootPath=currentdir.substring(0, currentdir.indexOf("ControlPanel"));
}else{
rootPath=currentdir;

[code]....