PT properties file does not contain the right path

[goreaditya]

The PT properties have hard coded path and does not get updated when copying over to the outputs file. Update the PT properties file in the input directory to fetch the paths set in the batch script and update accordingly.

[JimSullivan8997]

There is a new pt.properties file in an earlier commit that addresses this. However, it looks like an additional edit was needed to the class path in ptdaf.properties as well to get PT to work correctly.