working directory in web application

I have my Java project, say in C:\User\Workspace\myApplication
And theres an xml file in that folder: C:\User\Workspace\myApplication\myXML.xml

And in my java program, I will take that xml file to retrieve information. So, I need to call it from my program. And now I am loading that file like:
File xmlfile = new File(C:\\User\\Workspace\\myApplication\\myXML.xml)

And I know that its not a good way to load a file using directly the absolute path. So, I try to call it from my program dynamically. Here, my program is web application. And I use Tomcat.

First, I tried this way:

File directory = new File(.);
String loc = directory.getCanonicalPath();
File xmlfile = new File(loc + myXML.xml);

And, second I tried using: System.getProperty(user.dir);

Both first and second way give me the same result. When I tried to test those methods as Java application, they both gave me the path : C: \User\Workspace\myApplication

But when I tried to put it in my program which accepts input from JSP and run on server, then the result path is: C:\Eclipse. So, theres an error that the system cannot find the file.

Why it cannot find the actual path?
And how can I do it to load that xml file into my Java program.

Any reply would be greatly appreciated.