Flippers!! When is the best time to file for permits?

Hello Biggerpockets!

So my family and I have been flipping houses on Long Island, NY for about two years now, and starting to ramp up the business. One thing thats been we have yet to perfect is when to start filing for permits. In our area (and I'm sure many others), you need permits for just about everything (ie: plumbing permits just to uninstall old cabinets!). We would like to hear from other investors, how do you approach the permitting situation? Do you file during Due Diligence? Or just skip the permitting all together? Anything helps!!

Thanks, 

Mike