Question: I have an app built in node.js and I use the node inspector in order to debug.
But it's quite hard because of this:

1. My breakpoints are never saved after I restart the server
2. I cannot put a breakpoint on a file that has not loaded yet; so I have to step into from the first script to the one I want; REALLY PAINFULL!

How do you really debug node.js with node inspector? 

The videos on how to use node.js are quite misleading as everything is into a module...  

<http://www.youtube.com/watch?v=AOnK3NVnxL8> 

or this one the scripts appear are already loaded in the first script  

<http://www.youtube.com/watch?v=HJOH0-g8f6E&feature=mfu_in_order&list=UL> 

Edit:
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Nobody can answer this question? :s

Answer: 
You can use node-codein for inspection. It won't do runtime breakpoints but it should ease the inspection process.

<https://github.com/ketamynx/node-codein/>
Also worth noting.. vscode has a great debugger for node.

<https://code.visualstudio.com/> 

Available on Mac, Linux, & Windows.

It does runtime breakpoints (without the need of writing debugger; statements),
supports variable watches, and even has a call stack window (very nice).

Everything is so automated, it is now my goto over sublime text when using nodejs (and I LOVE sublime).