How to trace Drupal 7 Core Logic Using Netbeans with xdebug?
In my opinion, studying drupal core using netbeans and xdebug is somewhat too overwhelming. Starting in index.php will lead you through the whole bootstrap and other parts which do not need to be studied by someone who is starting to understand drupal. The most important parts to be familiar with are menu system and node system. These two parts are the basic building blocks on which you can build further (entities, taxonomy etc.). To study these, I would recommend the combination of 3 approaches:


Study the documentation 

menu - you can start with hook_menu (https://api.drupal.org/api/drupal/modules%21system%21system.api.php/function/hook_menu/7)
node api hooks (https://api.drupal.org/api/drupal/modules!node!node.api.php/group/node_api_hooks/7)

Study the examples module (https://drupal.org/project/examples) - it provides a lot of very well documented code which you can see in action (by turning on the module and its submodules)
Playing around with your own code snippets (=trying out what you learned)


I think xdebug comes later into this mix because it is a debugging tool (by definition) and even though jumping from function to function, from module to module can give you some understading of the flow of things, it is usually easier to just check it out in the documentation.