First, you must have diff tool. We use CSDiff (free), you can download here:
http://www.componentsoftware.com/Products/CSDiff/

I assume you have 2 indexu version: indexu 3.2 and indexu 5.0.1

Run CSDiff -> analyze folder -> select indexu 3.2 folder and indexu 5.0.1 folder -> Ok

You'll find a complete listing which files that are added, deleted, or modified. Click the filename to see line by line comparison.