Hi guys,

I've recently installed a magento 2.1 site, and trying to debug it; It's been HELL! I can get it to run, but EVERY 5seconds, Magento does some sort of JSON bootstrap call; continuously, hitting the main index.php file;

Its so important, that all info passing through this, so I can't ignore them. More and more system tend to use this mvc architecture, and how can I get PhpEd to work?

I need to debug the script, but always get interrupted; suggestions?

Help!

MVC is not what caused the problem at all. AJAX can be used everywhere, no only in MVC frameworks.
My understanding is that you were debugging a script in the IDE when client sent AJAX request and server started new debug session for it and hit the IDE. IDE in its turn had no clue if this session resulted from the script you were debugging or it was executed on timer in the browser or something else happened. So it offered you switch to that session and you agreed. You could disagree and session would remain in the background (see View->Debug Windows->Debug Sessions). You could even check "don't ask this question again" and your answer would be remembered applied next time without interruption.
On the other hand, instead of fighting with unintended calls, you can try to prohibit AJAX calls in the browser.
Alternatively you can re-direct such AJAX calls to a static page so they won't run any scripts and therefore won't bother you with debugger interruptions.
If you run Apache or similar server, you can redirect in mod_rewrite settings/rules.

Users can enable it for the storefront and the Admin panel through the configuration menu. To enable template path hints for debugging Magento 2 store, just login to your Magento 2 Admin panel, navigate to STORES > Configuration. On the left panel, under the ADVANCED section, click Developer